Doctor Who: The Equestrian Chronicles, Season one: The Beginning
by Dr TimeKeeper
Summary: After an unknown event in our universe, Junior must now learn to live in world where Ponies are the dominant species, will he find a way back, can he go back or will Junior have to deal with his own future decades later and all while caring for a recently re-crowned princess and a total of six brand new companions, it's going to be a heck of a ride AVANTI! LunaXOC
1. Episode 1: Arrival

Courier: Hi everyone welcome to my primary story. This follows the adventures of my Doctor Who Oc in the Ponyverse as he takes on the challenges of this world and a few of his own from his past _and_ future.

Disclaimer: I own nothing…NOTHING, apart from Dr What

Doctor Who:

The Equestrian Chronicles

Episode 1:

Arrival

**Ponyville, Equestria: planet Gaia: Year 1000**

**Golden Oak Library**

_It was a peaceful day in the land of Equestria, and no area was more happy than ponyville, there were many ponies who lived here but one was about to get a massive surprise._

"Oh, Spike I don't understand, why is the princess not doing anything. The mare on the moon will return tomorrow and she wants me to make friends!" the voice in distress was a young purple unicorn by the name of Twilight Sparkle, the personal student of Princess Celestia, the ruler of Equestria, next to the purple mare was a little purple dragon, reading a comic book, relaxing unlike his pony friend.

"Come on twilight, maybe it really is an old ponytale but you still have some tasks, so my advice is ill help you get those done and then you can return to your research" Twilight looked at her dragon, with shock in her eyes.

"Wow, spike I didn't know you could think like that, I thought food was all you thought about" she commented surprised by her friends use of his usually one sided mind

"and that" the mare rolled her eyes and was about to walk out the door when a strange sound could be heard, Twilight could not put her hoof on it yet to her it sounded like, Pain.

*VVROOPP VVRROOP VVRRROOPP VROOP CRAAAASH!*

"What was that!?" twilight exclaimed after the thunderous crash

"It landed in the west wing, come on spike" spike was terrified and wanted to run, yet he knew his owner would say differently.

"Don't you run away from things like this" twilight shot a glare at the purple dragon to which he followed the mare into the west wing of the library. "What is that?"

"I don't know seems familiar" to what spike was referring to was a large blue wooden box, that twilight thought that she had seen before, on the box was writing at the top (despite it being on its side) "police public call box, wonder what it is?" then as if on cue the doors swung open and out came a grey Pegasus with a crazy messed up mane and wearing ripped clothes that clearly did not fit anyway, the only item which seemed to be undamaged was a tartan tie tied loosely around his neck. Exiting the box, he tried to stand on his hind legs and attempted to wipe blood off his face not realising his hands where covered in more blood than his face, like he had just survived a slaughter or committed one, despite his appearance, he had a big grin on his face.

"sweet, a unicorn, never seen one before" the Pegasus was staring at twilight like she was some specimen, being observed, till he spotted spike "oh hold on, is that... no way A DRAGON!" and like a foul on his birthday began jumping up and down with joy...before falling on his stomach since he lost his balance, standing on his hind legs "ow, what the?, why did I fall over?" getting up he noticed his hooves and began to question his body "wait hold on, why do i have hooves?, AHHHHHH!, I'm a horse!, NOOOOOOOO!" Twilight was tired of his nonsense and began to try and get some answers.

"Would you stop and tell me who you are?" the strange pony stopped freaking and stared wide eyed at twilight.

"YOU CAN TALK!, THE f**K" he began freaking out again this time moving away from twilight, like we was staring at a monster "WHAT THE HELL IS GOING ON!" he then looked at his hooves then back at twilight with fear in his eyes _"what the hell am I"_ then as his voice lowered he collapsed unconscious followed, by golden vapour exiting his mouth. Twilight was shocked to say the least never had any pony reacted to anything like that before, spike however was still trembling.

"Twilight, what just happened?" the mare looked at her small friend and back to the supposed insane Pegasus lying on the floor.

"I don't know spike, but I say we wait for him to wake up, then get some answers from him" knowing that this pony was far too heavy for both twilight to lift, she decided to use her magic to teleport him to the couch. Placing a blanket and pillows by him to make him comfortable twilight sat there staring at the crazy pony, who reacted like he had no idea who he was, and the fear in his eyes, it was worse than a frightened foul on nightmare night.

"_What the hell am I?" _Those words rung in her head for what seemed like hours, not knowing what to do.

"_Maybe I should call princess Celestia...no I need to get some answers first" _after calming down spike both dragon and mare, left to complete the errands she was told to do.

**Sometime later**

Twilight returned to find her guest exactly where she'd left him, EXACTLY, he hadn't moved an inch. Sitting in front of him again, with her suspicion turning to concern, spike on the other hand had hoped in his bed for a nap, since he was still just a baby.

"maybe we should call a doctor what if he's ill" then the moment she finished, the Pegasus's eyes shot opened and he got up and looked around, scanning the area, finally his eyes resting on the purple mare in front of him.

"Did you call?" to twilights surprise he had the smile he had when he first exited his box, yet this time he was cleaned up and...

"_His wounds they healed up! not a scratch on him" _she thought, unsure who this pony was

"What's your name?" this pony was really strange first he freaks out about the most basic of things next the second he is conscience, he is asking personal questions.

"I'm Twilight, Twilight Sparkle" she answered him proudly.

"Well may I say that, that is a beautiful name, don't believe I've heard it before" though she would deny it she was blushing from his complement, no pony had ever commented on her name before.

"Well thanks, may i ask what is yours?" the pony gave a cheerful smirk, like he knew what was coming next.

"I'm The Doctor" twilight had cocked her head what an odd name, yet she believed that it was just his title.

"Doctor Who?" she asked thinking she didn't hear him correctly.

"Just that, The Doctor, I know it's confusing but I'm been going by that for centuries" he was beginning to show the craziness he had displayed before.

"oookkkaaaayyy, you're not going to freak out again are you?" the doctors eyes widened, not as much as they did last time, in fact he looked confused .

"What? Oh! No, no need to worry that was just a sever culture shock, I mean what would you do if your dragon over there could talk, ha-ha" he said with a chuckle not realising that Spike could indeed talk.

"He can" Spike said annoyed at the grey Pegasus.

"Oh snap, can all animals talk, or is it just horses and dragons" he said again surprised at a talking animal but unlike last time he didn't freak out about it.

"Pony, and no quite a few animals can talk, but they way you reacted, it was like you had no idea, who you were" on her statement, the doctor began looking around his body inspecting it.

"that because I didn't, I wasn't a horse last time a checked" twilight had noticed he kept saying the word horses, when pony is the correct term it seemed he was going to be a annoyance on that.

"Pony, you're a ..." before she could finish her sentence the doctor screamed like he did when he first saw Spike.

"Pegasus! I HAVE WINGS! AWSOME! And what's this, a tattoo? Interesting never had a tattoo before" he exclaimed jumping up and down, a bit like pinkie when she gets excited before staring at his flank.

"That's your cutie mark" the doctor had his confused face again, only this time he cocked his head.

"Come again?"Twilight turned around to show the doctor her cutie mark, which was 5 small stars, around a larger pink star, which was pictured sparkling.

"Your cutie mark, it's a sign to show what your talent is" she said lowering her flank.

"Well yours seems to match you well, sparkle by name and by talent" again a blushing twilight turned her head in embarrassment.

"yeah, I guess so" The Doctor got up, with some difficulty and attempted to open his wings to stretch which to her amazement, was a very impressive wing span almost the size of Celestia's wings " sweet Celestia" The Doctor looked at Twilight again with confusion.

"Who?" It was now her turn to be confused, no pony had not heard of Princess Celestia.

"You don't know who Celestia is" despite the seriousness for twilight, The Doctor didn't seem to care.

"Nope, but I'm sure to find out later on, now what's up?" he said now concentrating on Twilight's reaction.

"What?" the doctor rolled his eyes like he had seen the same thing over and over and was getting tired of it.

"Humans, horses, there's no difference! You said Celestia, when i stretched my wings, what about?" he raised his voice irritated for a bit before calming and tell Twilight about what he was going on about.

"Ohh! It's you have an impressive wing span, I've only seen one other pony to have a wing span that big" this seemed to tickle the doctors fancy as he didn't know he had such unique wings.

"Who?" He asked curiously

"Well...Princess Celestia's actually" The Doctor raise an eyebrow and brought his hoof to his chin.

"Well, going by your reaction to my wings, and the fact that this Celestia is a princess; I'm guessing she is your ruler" Twilight nodded to confirm.

"And my mentor" The Doctor was again confused but decided to save it for another day. "One more thing your cutie mark, can I have a look at it"

"yea sure" The Doctor replied cheerfully, turning to show twilight the mark on his flank "not had a good look at it myself to be honest" upon looking at his cutie mark, Twilight had no idea what it was for, the mark in question was a galaxy. "a galaxy huh, i was expecting an hourglass, or a clock"

"Well, what is your talent" The Doctor again put his hoof to his chin and began to think.

"Well, I myself expected time to be my talent, but now i think about it, time has nothing to do with it" Twilight was reconsidering the insane pony idea.

"What are you talking about?" she asked The Doctor now getting sick of him not making any sense.

"well, miss sparkle, the box I came out of is a time machine/spaceship and I know it sounds crazy, but she is rebuilding so you're going to have to wait, anyway my ship can go anywhere in the universe to any point in existence, but time is doesn't exist, it just what we use to keep a record of said existence, my talent isn't time fabrication but the ability to travel anywhere, any when in the cosmos I wish. That should sum it up" The Doctor explained this in about 30 seconds but Twilight seemed to be able to keep up with him, barley.

"Wow that actually made a lot of sense doctor" The Doctor then jumped up and landed on his four new hooves and attempted to walk "please don't tell me you don't know how to walk?" The Doctor had a frown on his face as he tried to get his legs to move the correct way.

"Like I said, I'm new to being a horse, not less than a day ago I was bipedal, now I'm a horse on all fours, plus I'm hungry" he revealed with a gurgling stomach in-between his explanation.

"Ok, I'll help you walk and get you something, in return you give me some answers deal?" She offered getting up and heading for the kitchen.

"On the food, deal, on the walking, no I've got it, it's just like crawling, only I haven't crawled, in over 400 years" he said revealing his age casually.

"Oh ok...WAIT! Did you say 400 years?" The Doctor looked at the shocked twilight, realising he should explain that feature.

"ahh, yea, might as well say I'm 464 years old" after Twilight calmed down, she made a few sandwiches and sat down next to The Doctor, ready to listen.

"Ok explain the basics" The Doctor cleared his throat after taking a bite of his hay sandwich.

"ok, my name is the doctor, I'm an alien to you, called a time lord, that box in the other room in my home/ space-time ship, called a TARDIS, which stands for Time And Relative Dimensions In Space, time lords are a race of, I would say humanoid, but it won't mean anything, anyway they are aliens who have, unlocked the ability to travel in time and space, since they live near temporal technology their live span became extremely long considering 100 years as being a child, but to top of the life span, we time lords have the unique, ability to change our appearance upon fatal damage to our bodies and so we change our physical appearance, the process is random and in result I have been turned into a Horse..." half way through his very long explanation Twilight had corrected him when he said horse instead of pony.

"Pony" The Doctor gave Twilight a look and decided to role with it.

"Pony, instead of the common bipedal-humanoid shape, so I have absolute no experience, as a...pony what so ever and it seems I am in a different world to my own as I have no knowledge of your history, and cultures. There done, any questions?" Twilight listened as best she could and now knew a bit about him be it not much.

"Actually, just one so far" she said calmly despite everything she had heard.

"What?" he said finishing off his sandwich.

"How did you eat, those sandwiches without stopping your explanation?" she asked pointing at the empty plate.

"I ate the first one, a bit the second and stuffed the last two in my jacket pocket for later, the one I was eating well, I'm a time traveller I probably stole it off myself in the future, speaking of its nearly sunrise, isn't there a party, thing going on" he said motioning to the window which viewed the moon slowly setting.

"Yea, the summer sun festival, when Celestia raises the sun for the longest day of the year, how did you know?" she asked wondering who he knew important events yet never being here before.

"well I read that book on rulers of Equestria, guessed it was what this place was called, and it said something about Princess Celestia's ability to raise the sun and moon, and well a galaxy is a celestial body, to I can tell the time of day, the weather forecast and the position of the sun in your solar system, by the way Celestia probably doesn't raise the sun, but instead turns the planet to face the sun" he said with a little smile on his face, he seemed really interested in the workings of Equestria.

"Wow, you are really smart" The Doctor gave a cocky smirk.

"I dabble, now this is a once a year event I would very much like to see it" Twilight was actually Glad she had made a friend like Celestia had asked, and with is knowledge, he might teach her a few things that even Celestia may not know.

"Sure, let me just wake up spike" The Doctor jumped of the couch on to the floor and continued to the front door.

"Don't bother, he got up and left a few minutes ago, when you were in the kitchen, I said we'd catch up later" he explained while getting up.

"you do think ahead" both ponies walked out of Twilights house and walked towards the stage that the ceremony would take place, both would continue to chat about different topics Twilight giving of a few giggles when The Doctor almost trips over.

**Ponyville Town Hall**

After ten minutes of walking The Doctor and Twilight walked to the crowd looking up at another chestnut coloured pony "that's the mayor, mayor mare" while walking Twilight told The Doctor about several ponies he need to know about.

"Wait, mayor...mare as in female hors...uhh, pony" he said with confusion almost forgetting to use the proper term.

"yea, believe it or not, I've not been here long, in fact I arrived today" The Doctor could tell that his new friend was happy as well as everyone else, but he felt something...off, looking up he saw the moon and several stars which moved closer behind the moon.

"Dam it!" Twilight saw something was off about The Doctor, in such a short amount of time he seemed, more serious.

"Doctor, what's wrong?" The Doctor turned to his purple equine friend.

"That book I read, it mentioned another mare that ruled Equestria and I think you knew already" that's when it hit Twilight like a hammer on her horn.

"The mare on the moon, how did I forget?" she yelled but over the mass of chatting ponies she wasn't heard.

"It was my fault, my arrival must have taken your mind off it" twilight was worried, till she realised that The Doctor actually believed in the mare on the moon.

"Wait you believe in the story" The Doctor had a serious look on his face that Twilight never knew he had due to his clumsy looking personality.

"in all my years, I have learned one thing about fairytales..." and if on cue the shocked reaction showed, something was not right "...and it's that they are always, always truth behind them" following his final words was purple smoke flooded the stage and formed a Beautiful mare in dark armour, with a coat as black as the void, despite her intimidating look, she was slim and elegant.

"Oh, my beloved subjects, it's been so long since I've seen you small little sun loving faces" fear had stricken everyone/pony, yet there was one certain rainbow coloured pony, was a bit too bold.

"What did you do with our princess?" Rainbow Dash shouted, being held back by the tail by Apple Jack.

"Hahaha, why am I not royal enough for you?" this dark mare was definitely the definition of the over the top bad guy, yet her mood was like lighting "don't you know who I am" Like a growing itch, another pony started commenting, a bright pink one to be precise.

"Ohh Ohh, more guessing games, uhh, hokey smokes, how about Queen Meanie, no! Black snootie, Black snoot..." Pinkie Pie that was known to never shut up was silenced by Apple Jack with an apple while who was still holding Rainbow Dash back. Yet the dark mare didn't pay any attention to her focusing on herself.

"Does my crown no longer count, know that I have been imprisoned for 1000 years" Twilight was getting agitated, seeing this evil mare terrorise innocent ponies no apparent reason.

"I have to do something" she began walking towards her, yet The Doctor stopped her remembering what someone had said to him, that no matter where he goes trouble will find him.

"No I will, I have experience in this sort of thing" he said coldly, not knowing much about how this world works he didn't want any harm to come to his new friend

"But you'll get hurt" Twilight had a vague idea of how dangerous this mare was but she didn't know him

"No I won't...trust me, I'm The Doctor" reassuring Twilight with his cocky smirk he walked through the crowd to face his new adversary

"Did you not recall the legend, did you not see the signs" out of the group of ponies one grey coloured Pegasus walked out, to confront her with a dark yet warm look in his eyes.

"I did and I know who you are, mare on the moon or better yet...Nightmare Moon" the fact this random pony had knowledge of the dark mare made most ponies gasp, as nightmare moon is, the fabled mare of nightmare night (Halloween).

"Well, well, well somepony who remembers me, so you know why I'm here" her movements and voice tone would scare a pony, but Nightmare Moon wasn't talking to a pony.

"yea, yea, yea you're here to bring eternal darkness and rule all of blah, blah, blah" The Doctor seemed to be treating this like a game, a game he played before, yet unlike his ruthless opponent he was one to show compassion "but I know what it's like to live alone for a long time, let me help you, this is not what you're meant to do" this seemed to strike a chord in the mare of shadows.

"You know nothing, and this is what I'm DESTINED to do, remember this day little ponies for it was you last, from this day forth the night shall last FOREVER!" every pony plus one dragon was frightened to the bone with the exception of the brave Rainbow and Time Lord.

TO BE CONTINUED

Next Time:

Night Time

Courier: thanks for reading and please tell me what you think in the review section, I would like as much feedback as possible

P.S. the chapters are subject to change every now and again, ether due to more compatible ideas or if it needs a complete re-write, if you visit my Twitter and Facebook Page, I will try to notify if I do update them

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	2. Episode 2: Night Time

Courier: Remember to put your comments in the review section

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Who:

The Equestrian Chronicles

Episode 2:

Night Time

_**Last time on**_

_**The Equestrian Chronicles**_

"_Oh, my beloved subjects, it's been so long since I've seen you small little sun loving faces" fear had stricken everyone/pony at Nightmares sharp voice._

"_Ohh, Ohh, more guessing games, uhh, hokey smokes, how about Queen Meanie, no! Black snooty, Black snoot..." Pinkie Pie said making a game out of the situation._

"_I have to do something" she began walking towards her, yet The Doctor stopped her remembering what someone had said to him, that no matter where he goes trouble will find him._

"_No I will, I have experience in this sort of thing" he said coldly, not knowing much about how this world works he didn't want any harm to come to his new friend._

"_But you'll get hurt" Twilight had a vague idea of how dangerous this mare was but she didn't know him._

"_No I won't...trust me, I'm The Doctor" reassuring Twilight with his cocky smirk he walked through the crowd to face his new adversary._

**Now the conclusion**

"Well, well, well somepony who remembers me, so you know why I'm here" her movements and voice tone would scare a pony, but Nightmare Moon wasn't talking to a pony.

"yea, yea, yea you're here to bring eternal darkness and rule all of blah, blah, blah" The Doctor seemed to be treating this like a game, a game he played before, yet unlike his ruthless opponent he was one to show compassion "but I know what it's like to live alone for a long time, let me help you, this is not what you're meant to do" this seemed to strike a chord in the mare of shadows.

"You know nothing, and this is what I'm DESTINED to do, remember this day little ponies for it was you last, from this day forth the night shall last FOREVER!" Nightmare cackled accompanied with lightning.

"then you leave me no choice" The Doctor had played this card far too often than he liked and knew he would have to stop her, yet the mayor and the royal guard had other plans.

"Seize her! Only she knows where the princess is!" the royal guard attempted to arrest Nightmare moon, but they should have known she was far too powerful.

"Stand back! You fools!" after repelling her attackers, she fled to who knows where, yet with the now free Rainbow Dash on her tail. Twilight walked to the brave stallion who had watched his new foe escape.

"Doctor what are you going go after her!"

"As much as I would want to, I can't, I don't know how to fly. But we need to stop her, come on let's get back to the library I need my screwdriver" with both Pegasus and unicorn running to the library, overlooking them was Rainbow Dash who fail to catch up to Nightmare moon in time.

"Where are you two going?" she said suspicious of the grey Pegasus

**LATER AT THE LIBRARY**

Spike who was found unconscious by Twilight lay in his bed, waking up only to fall asleep, after telling them to stop Nightmare no matter the cost.

"poor guy, his heart is in the right place, shame he is just a baby" The Doctor who still couldn't figure how to pick up his sonic screwdriver with a hoof, decided to ignore the logic and accept the impossible, and to his amazement he actually picked it up "but how, i have no bloody fingers!, what the F**k logic" as soon as he started questioning it the screwdriver fell "ok, ok, screw logic" he stated before picking it up again and putting it in his jacket pocket which he now had on, unlike his tie his leather jacket was damage but it had to do since he had no pockets, The Doctor was ready to stop Nightmare Moon, Twilight on the other hand.

*CRASH*

"Where is it, elements, elements how can I stop nightmare moon without the elements" she was tossing and turning every book she had with no avail.

"Twilight, as much as I love books, I don't think the location of anything as powerful as these elements of harmony would be in your average library book" and as if lightning its self was present Rainbow dash shot into the library and was right up in The Doctor's face.

"And just what are the elements of harmony! And how did you know about Nightmare Moon huh, you a spy?" The Doctor unfazed by the multi-coloured Pony didn't back down from Rainbows aggressive approach and stated walking towards her forcing her to move backwards, with the same force she used on him.

"We are in a library, you figure out how I know about a Power hungry horse, pony whatever, who is only ever mentioned in Fairy tales!" and with all his knowledge he still had to learn a few things, with Twilight happy to help.

"Doctor, their called ponytales" The Doctor raised an eyebrow then walked of cursing in another language. Just behind rainbow dash was Apple Jack who had just entered the library.

"Simmer down sally, RD he ain't no spy, but both of them sure know what's going on, dont'cha twilight and…" The Doctor rolled his eyes at the continued question of in his life

"Doctor" he said quickly and annoyingly

"Doctor wh..." Apple Jack was about to finish her question but was interrupted by a irritated Time Lord

"Just the doctor" not only was Rainbow and Apple jack here but other ponies that Twilight knew has also arrived "friends of yours Miss Sparkle"

"Um yea, Doctor this is Apple Jack, Fluttershy, Rainbow Dash, Rarity and Pinkie Pie" Twilight gave The Doctor the names of her new friends while every Pony greeted the Doctor in their own way, after the quick introduction, The Doctor decided to get straight down to business.

"Now , you want to help, fine glad to accept, but first I'm not familiar with a few things you find simple for example I'm older than all of you combined and I can't fly" this statement made Rainbow, giggle at how a fully grown Pegasus can't fly "anyway, I have just read, about these legends out of one book, Twilight here is the one who did most of the research, I also confronted Nightmare Moon as I have had past encounters in similar situations...minus the walking on all fours, these artifacts known as the Elements Of Harmony sound incredibly powerful and are the only thing that could stop her without causing lasting damage"

"What is that suppose ta mean" Apple Jack asked with a very strong accent which sounded like Texan.

"It means using the elements will stop her without killing her but I'm not taking chances, if the planet stays without the sun for too long, Equestria will die" the six mares could see the seriousness in his eyes and knew what he was saying was the truth.

"So we need to find out where the elements are and what they do" Twilight stated with concern till Pinkie burst the bubble in a good way.

"Elements of harmony, a reference guide" she read out, like it was hiding in plane site, contradicting The Doctor's previous statement.

"Ignore my statement, about powerful things in average books, seems everything logical in this world is irrelevant" he said before bagging his head on the wall.

"How did you find that" Twilight stated in disbelieve

"It was under E" replied Pinkie jumping up and down while The Doctor stood there gobsmacked

"Figures" he said to himself mentally face palmed/ hoof smacked himself, Twilight then pulled the book out and opened it, The Doctor walking up behind her reading the page aloud

"There are 7 elements of harmony, but only six are known kindness, laughter, generosity, honesty, loyalty and trust, the 6th is a mystery, blah, blah, blah, here we go the last known location of the elements was the original castle of the royal sisters, which resides in ...

**Jump 10 minutes, to the entrance to the everfree forest**

"_**The everfree forest**_" was everyone's (I'm going to go by human speech, I'm the narrator after all) reaction to the location of the castle, apart from Twilight and The Doctor.

"Apparently, Celestia chooses towns randomly" The Doctor mentioned calmly.

"Yes a different town, every year" Twilight confirmed.

"Then why do I feel like she didn't choose ponyville for its atmosphere, but for the fact that it happens to be right next to the castle, that this all started from" The Doctor had thought about this carefully, this Celestia seemed to be a great planner.

"Wee, let's go!" was Pinkies reaction, which continued to confuse The Doctor more than the hoof impossibility; no one alive is this energetic.

"Not so fast, look I appreciate the offer, but i really would rather do this on my own" Twilight was tightly focused on stopping Nightmare moon, which made The Doctor think about his past, he had always told people to wait for him to sort it, only to have them taken away.

"_No more"_ was the word his father had said the last time they met during the war.

"No can do sugar cube, we ain't going to let any friend of ours go into that creepy place alone" if The Doctor learned anything so far was that no matter what you do, Apple Jack could counter anything, yet the thought of friends made Twilight queasy, The Doctor could tell she didn't have many friends before today "we're sticking to you like caramel on a candy apple" a cold shiver fell down The Doctor's back and out his through wings.

"I sense a long future of apple related puns with you Apple Jack, don't I" he said before Apple Jack walked straight into the forest with the rest of the group leaving Twilight, The Doctor and pinkie who was also beginning to follow the group.

"Especially if there are actually candy apples in there" The Doctor and Twilight looked at pinkie with a blank expression "what those things are good"

"Twilight, something is bothering you, what is it?" The Doctor asked looking straight into the forest with the uneasy Twilight standing next to him.

"I'm just not used to having…friends" Hesitant to use the word flung around ponyville like currency.

"trust me you'll get used to it and you'll enjoy every minute you spend with them…400 years of travelling and I treasure my friend above even the brightest of stars" he reassured Twilight giving her hope for the future.

"Thanks Doctor, now let's go and save Equestria" yelling at the top of her lungs, motivated by The Doctors speech

"Avanti" The Doctor said to himself before following his brand new group of friends

**5 minutes later**

The six girls of the group, as only one boy was there, where all creeped out by the forest as it didn't look like it had been maintained in years.

"So none of you have actually been in here before" was Twilights attempt to break the ice.

"Oh, heavens no, just look at, it's dreadful" Rarity replied with her true lady like voice

"And it ain't natural, folk say it don't work the same as Equestria" Apple Jack added to the conversation with a chill from her spine

"Looks natural to me, in fact it's the most familiar thing I've seen since I got here, it just looks like the common forest in England minus the bad weather" The Doctor was the only pony actually admiring the forest as it reminds him of the many forests in his universe.

"Noooo poooony knooows, you know why?" Rainbow tried to scare everyone yet only half worked.

"Rainbow, quit it" Apple Jack tried to defend her friends, but she knew rainbow all too well.

"because every pony that has ever come in has never come OUT!" and on that note the ground cave in and all but Rainbow and Fluttershy fell, thanks to Docs inability to fly he decided to use his large wings to glide to safety, Pinkie and Rarity were caught by Rainbow and Fluttershy while Apple Jack caught a branch and Twilight hung by the edge, apple let go of the branch and tried to help Twilight.

"Let go" Apple told Twilight to let go as calmly as possible only to be bit back by the panicking Twilight.

"Are you crazy?" she screamed followed by a bit of the cliff breaking off.

"No I ain't I promise you'll be safe" Apple Jack was doing her best to reassure Twilight but it didn't have much effect.

"That's not true" still in a state of panic The Doctor Tried to steer himself towards Twilight to tell her she was going to be safe but instead he fell to the ground.

"Uh-oh, ahhhh!" he screamed as he fell

"now you listen here what I am telling you is the honest truth, let go and you'll be safe" now beginning to trust her as Apple Jack didn't seem the lying type, Twilight let go to fall several feet, then she was caught by both Rainbow and Fluttershy, with every one down safely, Apple Jack using her own skills to get down, and the doctor falling several feet and being the only one to take the full fall, slammed front first on the ground making it crack from the force

"Oww, everyone...ponies alright" The Doctor asked getting a nod from everyone and a smile from Twilight. Later on while all six ponies plus one Time Lord continued their quest Rainbow Dash was busy bragging about saving everyone except The Doctor who had a bandage on his head.

"Catching you in the nick, of time" Rainbow said finishing her glorified retelling of the event.

"Leaving me to fall to my doom, I told you I couldn't fly!" The Doctor shouting at Rainbow, both giving each other a evil glare.

"Yes Rainbow I was there, and I'm very grateful but we gotta..." cutting Twilight off was a large beast that seemed to catch The Doctor's eye

"A MANTICOR! I am one lucky guy!" The Doctor screamed like a little school filly jumping around at the sight of the beautiful creature, yet Twilight only saw it as an obstacle.

"We need to get past it" she declared motivating the others to take battle positions.

With every one trying to put it down and failing at it, The Doctor was too mesmerised by the creature and Fluttershy saw something was wrong but was too...well shy to say anything.

"Wait…WAIT!" everyone stopped at the unlikely event of Fluttershy speaking up, The Doctor now out of his trance could see the issue the beast was having. Walking back to the group, turned out that a thorn was stuck in his hand.

"How did you know that the thorn was in his hand?" The Doctor asked while returning to the group.

"I didn't, sometimes you have to show a little kindness" Twilight had heard her answer to the doctor question, but The Doctor himself did his thinking pose when he brought his hoof to his chin.

"Hmmm, honesty and kindness, Doc you are a genius" later on the girls plus The Doc, stumbled into a darker part of the forest.

"my eyes need a rest from this icky forest..." Rarity complained in her posh accent only to have darkness cover everything as if on her command "...didn't mean it that literal" after some minor arguments about pushing and shoving, the girls began to scream at the trees, which for some reason made scary faces, The Doctor who was completely disorientated by the sudden light from Twilights horn and the screaming, once he could focus again he saw that the girls were scared of trees which did look a bit weird, he would of hoof slapped himself if not for that pink pony laughing her face off.

"Pinkie run!" Twilight told her to back away, before she started... "Tell me she's not"

"She is" it seemed all the girls knew what she was doing so I'll see you in a few.

_**Intermission**_

Well, all the girls are laughing and The Doctor just didn't get it.

"I don't get it there just trees..." -_- "well at least that's laughter done, 3 down 3 to go" coming to a river the team discover that there is no bridge.

"How are we going to get across?" Twilight asked.

"Hold on do I hear crying" The Doctor was right, over to the left was a crying sea serpent with half his moustache gone "Ohh wow you my friend you look stunning" was The Doctors reaction to the crying sea snake till he noticed have his moustache was gone. "uh, minus the tash"

"Excuse me, why are you crying" Twilight asked the serpent.

"well, I was minding my own business when, some purple smoke, zoomed past and cut half of my beloved moustache clean off, I look simply horrid" The Doctor knew who was behind this, he also noticed that the most dangerous thing that had happened was the cliff "That's odd, for a being of darkness she's not very…dark, why do I get the impression these obstacles were made by a child" after some complements Rarity had given to the serpent she had enough.

"I simply cannot allow such crime against fabulosity go uncorrected" at that moment Rarity bit off one of the dragons scales and...Cut of her own tail, using her magic to attach it to the serpents face repairing, his moustache.

"Ohh, my moustache! Wonderful!" The Doctor stood in shock he actually liked the way Rarity had her mane and tail done, it was to him incredibly unique and today did not forecast a tail cutting.

"You look smashing" Rarity was pleased with her handy work, but Twilight was feeling sorry due to the loss of Rarity's tail.

"Rarity your beautiful tail" she said mourning the loss of Rarity's tail.

"Don't worry my dear, short tails are in this season, plus it will grow back" she seemed pretty calm despite crying on the inside, The Doctor who was still shock, shook his head and followed.

"Wait a minute! Fabulosity is not a word! Rarity!" running as fast as he could he finally reached his friends sitting by a broken bridge waiting for Rainbow to fix it she later flew back having finished the repairs and the gang having a look on there faces "let me guess ultimatum, them or us kinda thing" The Doctor was still suspicious about the incidents and was putting the pieces together far quicker than even he predicted "take that Sherlock, ha-ha"

"Yea pretty much, but i never leave my friends hanging" Rainbow proudly exclaimed before flying ahead

"At least we're here" The Doctor scanned the room with his sonic screwdriver for Nightmare Moon, just as a precaution while the rest picked up heavy stone orbs and set them in front of Twilight.

"Ok we have 6 where's the 7th" Rainbow asked impatiently.

"The book said that once all six are together, a spark would make the 7th appear, you know this reminds me of that anime I watched last week" The Doctor explained with precision yet complicated causing Apple Jack to interject.

"What the hay does that mean?" she stated unsure of what they were supost to do.

"I don't know, I'm a time travelling Pegasus, do i look like a princesses star pupil, ask Twilight" Twilight herself was not amused with The Doctor s attitude.

"I'm not sure, but i have an idea, stand back" Twilight got into position while the rest were lead out.

"Come on you lot she needs to concentrate" Apple along with everyone else where about to leave then she arrived.

"Girls, heads up!" The Doctor had seen nightmare appear and ran after her as well as Twilight, using her magic Nightmare teleported the elements, The Doctor and Twilight to the tower above.

**In the tower**

"Muhahaha" Nightmare had the elements and Twilight was ready to fight, but a certain Pegasus decided against it

"No Twilight you get out of here, I'll hold her off... and before you say anything remember what i asked you back at the ceremony" looking into his eyes Twilight saw it, the darkness he had inside him, anger, sorrow, regret, he had seen conflict before and he never wanted it to happen again.

"_Trust me...I'm the doctor" _Understanding what he meant Twilight ran off to the side, leaving both Nightmare and The Doctor face to face.

"Stop this, nightmare, it's not too late, think about what you're doing, you could destroy, everything" it was clear that Nightmare Moon was not taking him seriously.

"You're kidding, you're kidding right" she said confident that he was bluffing and just scared of her tremendous power

"I wish I were Nightmare, you may be older by thousands of years, but I'm still pretty old, I know the pain of loss, my entire race is gone!, I don't belong here and I can never go back!, I will never see my friends or family agian!, YOU THINK IM KIDDING! WELL HERES A NEWS FLASH, MISS BAD DREAM, IM A TIME LORD YOU ARE A HORSE, I'VE FOUGHT IN WARS THAT NEARLY DESTROYED UNIVERSES, I HAVE SAVED MORE LIVES THAN ANYONE CAN COUNT" The Doctor had lost his temper and was about to unleash it all in a duel between two forgotten legends "YOU DON'T SCARE ME, and do you want to know why?" The Doctor's outburst affected everyone who heard it, Nightmare especially, it was like she felt his anger and he was telling the truth

"Why?" Nightmare asked with confidence, which lit the spark in his hearts, he was back pony or not

"Because I. AM. THE DOCTOR. And you've been played" his confidence was well placed as Twilight had used his distraction to sneak past her.

"WHAT!" looking behind herself she saw Twilight sparking the elements "_how did I not see her, I didn't feel her magic. It was like another was masking it but he is a Pegasus he can't have magic!" _ Nightmares attempt to stop Twilight would have failed but as if bad luck gave its blessing the elements did...

"Nothing!, that's it" The Doctor and Twilight were gobsmacked, their last hope was destroyed and with an evil cackle and a stomp the stones shattered.

"You little fools, thinking you could beat me! Now you will never see you princess or your sun, the night will last forever!, muhahahahaha" The Doctor was distraught but he knew it wasn't that easy, it never was

"Let me tell you a secret Nightmare, my promise" The Doctors said helping Twilight up from when Nightmare shoved her out of her way.

"What was that a promise to a little filly, pathetic" she asked not knowing of the darkness that lay in his heart, a void blacker than even Nightmares majestic night sky.

"No, to myself, as you may have guessed The Doctor is a title not a name, but to me it is my identity, over 300 years ago I made a promise to never be cruel or cowardly, TO NEVER GIVE UP, NEVER GIVE IN THAT IS MY PROMISE! And as long as my hearts beat and I have friends to back me up i will never break that promise" behind both Twilight and The Doctor were the others, who had heard The Doctor over the lightning which gave Twilight the spark she needed.

"You think you can destroy the elements of harmony just like that, well you were wrong" Twilight was now as confident as her Ageless friend giving him a final idea.

"That's right, because the power of the elements are right here!" The Doctor now able to hatch the plan he has been cooking since the beginning of the forest, and then the pieces of the elements began to lift, causing Nightmare to worry

"What?" she said unsure what was happening?

"Apple Jack, who reassured me during hard times, represents HONESTRY" then three of the shards made their way to Apple Jack and several of the others. "Fluttershy who tamed the manticore with her compassion represents KINDNESS, Pinkie Pie who vanished fear by giggling in the face of danger represents LAUGHTER, Rarity who calmed a gentle serpent by giving something meaningful represents GENEROSITY, Rainbow Dash who would not give up her friend for her own desires represents LOYALTY and The Doctor who helps any and all who need it without a second thought sparking hope to everyone who meets him represents TRUST, the spirit of these six ponies, got us through every challenge you threw at us" nightmare was totally gobsmacked at the fact that each one of her adversaries represented the very elements that imprisoned her

"YOU STILL DON'T HAVE THE 7TH ELEMENT!" Nightmare was on her last legs, trying to get desperate.

"Sorry Nightmare, but we do, I don't know a lot about this world but I know that it is held together by a force even I'm yet to understand MAGIC" The Doctor and Twilight now had the power of the elements of harmony and now intended to use it. To assist the team the elements took new forms for practical use, the five mares elements turned into golden necklaces, with the element housed in taking the shape of the cutie mark of each mare, with The Doctor's turning into a helmet that when worn made him look like a Alicorn (which is what Nightmare Moon is) with the symbol of the galaxy on the side and Twilights took the form of a crown with the element houses as the crown jewel and with the power harnessed the energy passed from the five mares to Twilight to amplify the power then focused and fired through The Doctors new horn, engulfing and defeating Nightmare moon. It was over.

After the battle, all the ponies awoke with a massive headache

"Oww, my head" the first voice to speak being Rainbow Dash.

"Every pony ok?" Apple Jack was the first to check everyone was ok.

"Isn't that my job, i am a doctor you know" The Doctor got up and rubbed his head as all that power was focused through it felt like a hammer to the brain.

"Thought you said it was a promise" Apple was now teasing The Doctor about his little secret.

"It is! but I have a medical degree as well and no I'm not telling you my name!" everyone could see that the relationship between Apple Jack and The Doctor would be interesting to say the least

"Thank goodness!" Rarity was excited to find that her tail had grown back.

"Well at least some pony's happy" was all Rainbow could say to the fashion designer.

"Hey I tell you what I never thought we actually represent the elements of harmony" Apple Jack was now admiring the necklace around her neck.

"that you do" a voice could be heard from out of nowhere followed by a bright light being the sun which had risen once again and in the light stood a majestic Alicorn with a rainbow coloured mane (a lot lighter than rainbows), all of the ponies bowed in respect but Twilight and The Doctor who had no idea who she was, but he got the idea that this was the ruler of Equestria Princess Celestia plus she was not his monarch to bow too, he did not belong here after all.

"Princess Celestia!" Twilight ran to her teacher glad that she was safe.

"Twilight Sparkle, my faithful student, i knew you could do it" Twilight was confused as she didn't not understand the way her mentor had planed the return of Nightmare Moon

"You said it was just an old ponytale" she said remembering the letter she had sent Twilight before she came to Ponyville.

"I told you to go make some friends, I saw the signs and I knew you had the magic inside to defeat her but you could only unleash it once you let true friendship in your heart" while Celestia was speaking with Twilight The Doctor had made his was towards the defeated Nightmare Moon, yet in her place was a young Alicorn the size of a filly she had night blue coat and a sky blue mane.

"Are you ok?" The Doctor asked the young mare who had terrorised millions all because of jealousy.

"Stay away!" the mare was clearly frightened, which proves that she had little control of her actions as the dark mare.

"Hey, I'm not going to hurt you, I just came to help, like i said i would in the first place" coming up behind The Doctor was Celestia for whom it had been so long

"Luna, it had been too long since I've seen you like this, it time to but our differences behind us we were meant to rule together little sister" Celestia revealed the fact the Nightmare Moon was her sister and that her real name was Princess Luna.

"SISTER!" was the reaction from everyone but The Doctor, who stood there looking at his new found friends with a blank look.

"Oh, come on you didn't see this, one controls the day the other the night we are standing in the castle of the royal sisters for goodness sake plus their both Alicorns" The Doctor actually hoof smacked his face this time before turning back to the two reunited sisters.

"Please come back Luna, will you accept my friendship" everyone was hoping she would accept and not explode into Nightmare Moon again, yet The Doctor had one last trick up his sleeve so make her stay as a protector rather than a conqueror.

"I'm so sorry, I've missed you so much big sister" Luna exclaimed with tears of joy flowing down her eyes along with her sister, who was happy to be with her once more after 1000 years.

"I've missed you too" and that is the story of how The Doctor along with the mane 6 reunited the royal sisters. Now take it away Pinkie.

"This calls for a PARRRRTTTTTTYYYY!" with the day restarted, Ponyville celebrates the defeat of Nightmare Moon and the return of Princess Luna (classic evil imprisoning a relative had to be defeated for release kind of thing, no one made the connection), with Celestia talking to Twilight about living arrangements, The Doctor walked over to princess Luna who was watching the celebration.

"Here, 1000 years on the moon is bound to create a large appetite" The Doctor gave one of the Sandwiches that Twilight made for him to Luna, who took it wondering why this pony was helping her "Why not go over there?" despite her happiness being reunited with her sister Luna, still felt miserable.

"After what I did to them, they would never forgive me" she said dropping her head down in sadness.

"actually you would be surprised, I noticed that you were not in complete control but you knew about the elements, so you influenced Nightmare to setting traps that would test the embodiments of friendship and I'm not one for that kind thing but I do know that they have forgiven you, trust me on that one ok, now eat up" The Doctor did make a lot of sense to the princess and because of that her mood brightened up and she took a big bite out of the sandwich and was surprised at its taste, she had never tasted anything like it.

"Thank you Doctor" she blushed at the weird Pegasus who tried to help her when she wasn't herself and she admired him for it.

"Oh and one more thing" The Doctor said stopping and turning her head to face Luna.

"What is it?" She asked wondering what he had to say.

"the truth of the night, it's not there to be shunned and it never was, it is the night that people take shelter and sleep because they know they are safe to do so, now they can sleep easier knowing they've got you watching over them now, you protect the people when they are most vulnerable, also with a job like Celestia I think she needs some sleep don't you think...good luck Luna" and with that The Doctor walked away from the celebration wondering what he was going to do next.

Next Time:

Golden ticket vs. lunch

Courier: so how was the first part of season one? Want more? Then read on cause this won't end till MLP does and this may even evolve beyond that.

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	3. Episode 3: Golden Ticket Vs Lunch

COURIER: Back again with episode two of Equestrian Chronicles and this is no doubt gonna be my longest story as its supost to follow every episode including the move Equestria girls which I would like to do, but since some episodes are just the odd character trying to do something like the Cutie mark crusader episodes, will not be written in order maybe as a side project after I got though the season that it is in.

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Who:

The Equestrian Chronicles

Episode 3:

Golden Ticket Vs Lunch

It had been a week since the events that took place at the summer sun celebration and the return of Princess Luna; everyone was getting back to their routine but the Doctor who still struggled to adjust to pony life decided to help AppleJ and Twilight with some apple harvesting.

"Thank you kindly for helping me out Twilight, you too Doc. I bet Big Mac that I could get these apples in the barn by lunch time," Apple Jack was in a cheerful mood as she always was with the Doctor and Twilight in tow along with Spike who was picking out different apples looking for one to eat "if I win he's gonna walk down town wearing one of grannies skirts" Apple gave small laugh at the image of her older brother in a skirt.

"No problem at all Apple Jack" The Doctor replied looking away from the little dragon throwing away all the apples.

"Glad the goal is lunch time, all this hard work is making me hungry" was Twilights response clearly seen with hunger in her eyes.

"I know right" Spike commented throwing an apple behind him hitting Twilight on the head which resulted in twilights death glare on Spike.

"You've been lounging on my back all morning while we worked" disappointment in Twilights voice.

"Exactly, you were taking so long I missed snack time" Spike moaned like a child…or a human child.

"well you should of said Spike, I would of given you a ruby or something" The Doctor had read several books in his free time and packed his newly made dimensionally transcendental bag to meet certain requirements like a gem stash for Spike as he learned that dragons eat them as a delicacy "it's what I packed my bag for anyway" but before Spike could respond he pulled the perfect apple, a bright strawberry red glowing in the sunlight Twilight stared at it with lust.

"Wow Spike that looks delicious" and as quickly as it was shown it was gone "Spike!" The Doctor shook his head and gave a smirk.

"and you just lost a nice apple sized ruby I got for you, too bad" he then trotted past them with a smile as Spike looked in disappointment just before he looked like he was going to barf and like a personal letter box, fire burst from spikes mouth and transformed into a letter "well that's handy, whose it from" The Doctor commented as he had never seen Twilight get a letter from Spike stomach before.

"It a direct line to Celestia, it how we communicate when he are away from each other" Twilight explained as Spike jumped up to receive the letter. During his first day The Doctor did not see Celestia that often, but when he left after the battle for eternal darkness (as The Doctor liked to call it) Celestia came to him for a chat.

**Twilight's house, summer sun-day**

The Doctor did not have a key to Twilight's door so he used his screwdriver to open it and proceeded to the west wing. before he could enter the Tardis which was now upright (convenient) and looked better than ever with brand new shade of blue, a tall mare walked up from behind him.

"you are The Doctor I presume" turning his head he saw Princess Celestia, her main was definitely her best feature as it flowed perfectly unlike his hair during the time war which would never sit straight, unlike most who would bow he did not as she was not his ruler.

"Yea that's me" he answered with a smile which made Celestia giggle.

"It seems your reputation precedes you, Twilight as spoken all about your bravery to protect her and my subjects from my sister" she spoke with the expected royal kind of accent but she also had a 21st century feel to her voice.

"It's my duty to help. I saw many worlds fall in my life and I vowed that none shall ever fall again and this place is no exception" he reassured the princess as he unlocked the door to his TARDIS. (holding a key with hooves …logic anyone?)

"So I assume we can trust you to defend Equestria when the need arises?" she asked finally causing The Doctor to think about his life. From the war to this moment he had to make a choice, leave like he always did and find a way back or stay and protect this universe as a guardian of harmony; he turned his head to face the monarch who had a gentle smile on his face one he had not seen since his mother…

"Yes, you can trust me princess I will defend Equestria with my lives, you can count on it" he said with pride in his hearts and smile on his face. _"goodbye father, Willow, John, we will met again"_

**Present day**

Done with his flash back, looked down to see Rainbow Dash and Apple jack fighting over…

"Spike, what are they fighting over?" without looking the small dragon gave him two golden tickets which had on them "ticket for one, the grand galloping gala?..." raising an eyebrow he gave the tickets back "what I weird name, fits but still weird. So let me guess Twilight got one and a spare and now Dash and Apple are fighting over the ticket" he asked which spike followed with a nod.

"we'll look at that, I don't know about you but I can't think on an empty stomach, so I'll think about it over lunch and I'll get back to you two ok" as Twilight walked away The Doctor followed feeling peckish himself with Spike on his back while behind them Apple and Dash began a hoof wrestle.

Later on in ponyville The Doctor and Twilight with their dragon sidekick Spike walked though town looking for a place to eat.

"So who are you going to give the ticket to Twilight?" The Doctor asked with a worried look, he knew that the one thing harder than a life or death choice is a choice of which of your friends go somewhere with you.

"I don't know Doctor but I really can't think straight when I'm hungry, so where should we eat" and at the most unlikely of times a pink bursts out a door and into the trio. After the tumble the two tickets floated in the air lightly landing of the nose of the infamous pink party pony, Pinkie Pie.

"Ahhhh something on my face heeellllp, wait! These aren't" stopping for a minute to confirm her eyes the only part of her body that wasn't pink "TICKETS TO THE GRAND GALLOPING GALA!" then she started singing followed by The Doctor ears turning off "Ohh thank you Twilight, it's the most wonderful gift ever" both purple and grey ponies stared at the ecstatic Pinkie as she though the ticket was for her.

"well at least Rarity hasn't seen them yet" The Doctor said at the wrong time as he picked up the tickets only to find the heavenly white unicorn standing in before him.

"Are these what I think they are" she said with disbelieve.

"Bollocks" was all the Pegasus could say taking a few steps back from the clearly dangerous, generous beauty in his presence.

"Yes, yes, yes, Twilight is taking me to the grand galloping gala in canterlot" was Pinkies answer to Rarity's question followed by a sparkle in the white unicorns eyes, mane too.

"The gala…I design ensembles for the gala every year but I've never had the opportunity to attend, oh the society, the culture, the glamour, it where I truly belong" she said with the posh accent at its maximum.

"Of course you do" The Doctor hoof palmed himself with his sarcastic comment.

"And where I'm destined to meet…HIM!" again followed by a hoof palm.

"of course you are…again humans and ponies are mentally no different" he said before walking off as Rarity explains her supposed fool proof plan at a royal wedding "you know in my universe every little girl has the same dream and like you they will fail, in fact if any one of you becomes related to a royal family i will pay you 100 bits" not realising he had made a terrible mistake for the days to come.

"still I cannot believe you would invite Pinkie so she could "party"" saying it like it was frowned upon "and prevent me from meeting my true love, how could you" she said finally turning away with her nose up and like the world was trying to give The Doctor a double heart attack a small white rabbit shot up and nicked one of the tickets and ran to give it to Fluttershy.

"The thing is I haven't decided who will get the extra ticket" as soon as Twilight mentioned this, both Pinkie in disappointment and Rarity in excitement, responded how anyone would really act.

"YOU HAVEN'T!" both ponies exclaimed accordingly, than a very quite yet gentle voice spoke up.

"Uh, excuse me…Twilight, I would just like to ask if it would be alright, if you haven't given it to someone else" but Rarity was surprised, as Fluttershy was godly shy and she assumed she couldn't possibly have a reason to go.

"You!, you want to go to the gala?" she said raising an eyebrow which then Fluttershy when on to explain her reason for wanting the ticket, however The Doctor had enough and decided to head to what looked like a burger place. about a couple of days after his arrival Celestia had kindly given him a small allowance to buy certain things like clothes and equipment, so he kept his wallet on him in case he needed something. After entering the restaurant which was called the hay shack, The Doctor examined the menu, it appeared that all the food ponies eat was considered healthy for horses on Earth but the hay shack clearly resembled a fast food joint, then a bright green mare with orange hair (yes orange, not ginger) looked at the grey Pegasus with a smile from behind the cash register.

"Hello, sir may I take your order" catching The Doctor 's attention he made his way over and made his choice.

"Yea, sorry can I have a big hay with…is that cheese?" he asked not knowing if ponies collected milk.

"Yes sir, that is a big hay with cheese and anything else?" she asked resulting in The Doctor checking the drinks.

"If you don't mind me asking what is in apple cider?" the young mare raised an eyebrow as the stallion acted as if he was just learning what was in the food that he ate.

"It is one of the apple family's tuned down recipes, so it isn't as strong as the home made one" after a brief explanation The Doctor was finally satisfied.

"Then I'll have a large one of those as well, seems I'm a lot more thirsty than hungry" this seemed to be his signature trait for mares as the cashier gave a small giggle at The Doctor's goofy charm.

"of course sir it won't be a minute" after his food had arrived he decided to walk back to the library and eat there. About have way back he stopped in his tracks to see Twilight running past with what looked like the entire female population of ponyville proven be the cashier that served him also in the mob.

"Well seems the entire town knows now, poor Twilight" after they passed The Doctor crossed the path only for another group follow up behind them and trample over him leaving him near cripple on the floor with his precious lunch only an inch away "must reach food!" he said with pain in his voice only for a small filly run past stepping in the bag crushing the food and spilling the cider, the little one stopped realising she had stepped in something and her reaction proved she was sweetie belle, Rarity's little sister.

"Eww, I stepped in someone's lunch" looking back to see a horrified grey Pegasus as his eyes where completely dead "oops, sorry mister" getting up from the ground looking at his destroyed salvation he stood on his hind legs only to collapse on them again

"NOOOOOOOOOOOOOOO!" he screamed at the loss of his last hope of removing hunger and thirst.

_**Later on at Twilights house**_

After returning to the library The Doctor collapsed on the couch being the Time Lord equivalent for starving, he decided to sleep and get some dinner when twilight came back. He began to close his eyes when I bright flash blinded him for a brief second, upon his returning vision he saw Twilight and a scorched Spike rushing to close all windows and dim the lights.

"Twilight, that won't work because…" before he could explain the lights turned back on and their friends were right behind them.

"Oh for Celestia's sake, I can't decide as your all my friends and I can't let one go without the others being angry or sad" Twilight was on the verge of a mental break down and all six of her friends could see that that.

"Twilight sugar, I didn't mean to put so much pressure on you and if it helps I don't what the ticket no more, you can give it to some pony else, I won't feel bad, I promise" AppleJ's little speech drove the rest to tell her that they didn't want the ticket ether apart from Rainbow at first.

"We're sorry, Twilight" the five girls spoke in unison however there was a very irritated and hungry Time Lord also in the room.

"Well it's your greed that cost me my lunch, well actually it was Rarity's sister but that's cruel blaming a child so I blame all of you, you own me a big hay" after the apology and The Doctor's little outburst she stood up and signalled Spike.

"Spike take a note, dear Princess Celestia, I've learned that joys of friendship is sharing your blessings but when there is not enough blessings to go around having more than your friends can make you pretty awful, so I appreciate the invitation, I will be returning both tickets to the grand galloping gala" this caused every one Doctor excluded to gasp in shock.

"WHAT!" they all shouted in unison.

"I my friends can't all go, I don't want to go ether" The Doctor had seen that Twilight was a pony of her word, but he had something crawling in the back of his mind.

"Hey I've just realised, if the Princess is your mentor and you know her pretty well won't she be able to just give you extra tickets" he said as spike sent the letter making everyone else think.

"Ya know what I think your right doc" Apple replied as Spike began to barf, blowing out green smoke which turned into a letter and almost taking Apples head off "whoa Nelly"

"well speak of the devil" as the letter landed all, the girls turned, unsure of his comment "it's a saying, you know when you're talking about someone and then they show up or they are mentioned…never mind" all they girls laughed as The Doctor just gave up in his attempts and opened the letter "My dearest student Twilight why didn't you just say so in the first place, SEE! I told you, you could of just asked anyway here are 7 tickets to the gala" all the girls gasped causing The Doctor to hoof palm himself again.

"You really need to stop doing that" Spike said to his grey friend.

"Can't help it, these girls are just bloody thick sometimes" he said before handing out a ticket to everypony leaving one in his hand.

"Allow us to treat you to dinner" Rarity told Twilight as they all left with their tickets apart from Spike who began walking up stairs.

"Spike" the little purple dragon who felt left out as he didn't get a ticket turned to face The Doctor "here take it"

"Huh?" Spike said confused as Twilight had a reason to not go but The Doctor didn't.

"I don't want it, and I think Celestia knew that so this one is yours" taking the ticket, Spike ran out the library with a childish laugh passing AppleJ and instantly dismissing his desire to go, with Spike barfing up yet another letter with a tag on it.

"Hey Doc! it's for you" the little dragon gave the Pegasus the letter before running off, curious he opened it, it read.

_**Dear Doctor**_

_** I understand your desire not to go to the Gala but would you please attend as I will be busy with the guests and Luna will be alone the entire night all I ask is that you give her some company.**_

_**Yours sincerely Celestia**_

_**P.S. I would suspect Luna would appreciate it if you turn up, she seems to have taken a liking towards your kindness when you first met.**_

In the letter was another ticket which The Doctor placed under his tie and walked off towards his friends.

"Seems like I'm going to need a new suit. RARITY! I NEED A FAVOUR!" He shouted to the white unicorn while they all trotted to the nearest restaurant.

Next Time:

Sonic-Time Boom

_COURIER: Thank for the support, everyone and I would like to take a mo explaining the episode order as next takes place after the sonic rainboom episode and is like half a series way._

_DOCTOR: Yea why is that anyway?_

_COURIER: I'll tell you, you see the every season takes about 23-26 episodes, apart from season 3 which was 13 and a movie, but so I have time for more original adventures I'm only doing episodes that are connected to the final two-part finale or if they are really good and maybe if people vote for one. So I have to admit I didn't like this episode much but it is connected to the key point of this story which is a bond between both the Doctor and Luna._

_DOCTOR: Wait, what? Me and Luna._

_COURIER: She didn't get enough screen time and I like the similarities between her, The BBC Doctor and My Doctor as all three live in their shadows and have dark legends of their own._

_DOCTOR: Oh, ok cool, any way if you have any questions for me or Courier, just visit the brand new Tumblr page at _

_COURIER: Need to use it for something, however I have limited knowledge of Tumblr so, if you don't have Tumblr just pm me but I would prefer on Tumblr…OH and one more thing this chapter in the Chronicles Saga is the one most people like (which makes me happy) so the more people read the faster I make stories and give me some ideas for episodes if you want I just won't tell which ones I'll use if any thanks again. Bye guys._

_DOCTOR: See you._

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	4. Episode 4: Sonic-Time Boom

_COURIER:_ Hey guys this is a story I've had under my hoof for some time, it's just to show that The Doctor isn't just brains when in a dire situation. It also builds up the development of the bond which is forming between Luna and The Doctor. Well enjoy

Disclaimer: I do not own MLP: FIP OR Doctor Who and I'm only doing this because I want to

Doctor Who:

The Equestrian Chronicles

Episode 4:

Sonic –Time Boom

It has been a couple months since The Doctor had landed in ponyville and helped the mane six defeat Nightmare Moon; it had been a very interesting day for him as a contest for best flyer was being held in Cloudsdale and since he was a Pegasus he decided to go and cheer for Rainbow Dash (considering that the only other Pegasus was Fluttershy, he thought it was the smart thing) but later on everyone could come, yet Rarity had grown some butterfly wings (courtesy of Twilight) which in the process made Rainbow more nervous than she was. During the contest, which the first prize was a day with the Wonderbolts, Rarity entered at the last second and ended up showing of her wing which had dissolved in the sun causing the Wonderbolts to intervene but ultimately Rainbow had forgotten about the contest to save her friend.

"Hold on Rarity!" as everyone marvelled at her speed, The Doctor knew what would happen (he knew nothing of the sonic rain boom outcome).

"Doctor are you ok?" Twilight asked The Doctor who had his head almost below the balcony, hoping he wasn't going to be sick.

"Twilight! You don't understand! At the rate of her velocity and her wings giving the right momentum!" The Doctor shouted in Twilights face with glimmer and joy "she could break the sound barrier, producing a SONIC BOOOOOM!" and as he finished Rainbow had indeed broken the sound barrier and the colour of her mane was all that remained as the sonic boom and the trail behind her was a perfect rainbow. Now knowing he could potentially break the sound barrier, The Doctor had an idea.

**A WEEK LATER**

Sitting on a cloud The Doctor was applying bandages to his head and legs while he was doing so didn't notice Rainbow Dash creeping up behind him.

"Uhh, Doc what are you doing?" The Doctor turned to face the rainbow coloured Pegasus.

"Well, Rainbow I am a scientist and watching you break the sound barrier was something I never considered, so I am attempting to do the same, but I did fail a couple of times" he explained showing Rainbow all his bruises.

"Well, I am pretty awesome, but I don't think you can do a Sonic Rainboom, no offence?" the stallion of time gave a quick smirk.

"None taken, and I'm trying to create a normal sonic boom, the rainboom is unique to you and you alone. You see when anything breaks the sound barrier, they become too fast to see clearly so their colours follow them, since your mane is Rainbow coloured you produce a sonic rainboom" enlightened by her small lesson Rainbow Dash forgot what she came for.

"Oh yea I forgot, Twilight told me to get this too you urgently" she handed him a letter stamped with the royal seal also giving him a salute.

"My faithful student Blah, blah, blah, I require you and your friend to come to Canterlot urgently" after reading the letter he stuffed it in his bag and both time and rainbow ponies raced to the capital of Equestria, it was obvious that The Doctor was now used to his wings and had grown to flying so well that he could almost keep up with rainbow at full speed.

**OUTSIKRTS OF CANTERLOT**

Once within eye sight of canterlot, it became apparent that something bad was happening as the castle was damaged and buildings were burning and collapsing.

"What happened here?" Rainbow was shocked, at the revelation before her eyes.

"I don't know, Rainbow go ahead and help out, I need to see Celestia" with Rainbow breaking off the doctor landed in the castle via the big hole into the throne room, inside he saw princess Celestia comforting Luna, who looked gravely sick with her night blue coat's colour fading in and out "Celestia!, what is going on?" Celestia's face was full of concern, knowing that she was faced with an ultimatum.

"Doctor, it's Luna, she is terribly ill and can't control her magic which is causing destructive waves of energy, but I can't leave as the first time it caused most of the damage you see now" The Doctor knew her situation and was thinking of a way to fix it, mainly for Luna as she was the source to helping her would allow time to recover and repair the damage.

"Ok, let me have a look at her, I've read enough on pony anatomy to be an actual doctor for ponies" taking off his bag he pulled out several medical tools, Luna tried to speak, but she was too weak to even move and struggled to say anything.

"Doctor?" she asked recognising his voice. He then began examining Luna.

"Don't speak Luna, save your strength, don't worry you're going to be fine" The Doctor reassured Luna and she closed her eyes resting, with a small smile on her face. Celestia however was worried about her sister, afraid that the city would shun her since she was the most feared pony in history, reformed of course, that had almost destroyed part of canterlot.

"Will she be alright?" The Doctor took out a thermometer from Luna's mouth, it surprised her that Luna was actually letting The Doctor help her _"she wouldn't even let the royal physician come near her yet she allowed him to help her, he didn't even have a medical degree…so that's why he represents the element of trust"_

"She's not good, it looks like she's fighting an infection" The Doctor could of helped her if the damage was physical, but he knew nothing about illnesses to ponies "Celestia, did you have her examined after she returned?" Celestia knew this sort of thing would happen.

"No, I tried, but she wouldn't let anypony near her when it came to medicine, in fact you're the only doctor to examine her. The Doctor placed his hoof on his chin and began to think, and then it hit him.

"Hold it, Princess I'm guessing that, the medical technology of today wasn't present 1000 years ago"

"You are correct" she confirmed realising were he was going with this "know that you say, she hasn't aged, since her banishment"

"So, which means that she is ill with a disease, that was present a millennia ago, that would have not had time to take affect" the princess now knew what had made her dear sister ill.

"No! The Discord fever! How could I be so blind?" The Doctor had no idea what she was on about, but by the sound of her voice, he knew it wasn't good.

"Why do I get the feeling this was mistaken by disco fever" ignoring his comment the princess used her magic to bring a book, which was very old but well maintained, opening the book to a page near the back.

"It was an illness made, by a wicked being known as Discord, he was the embodiment of disharmony and chaos and had the ability to control the fabric of reality, after his defeat an illness soon appeared Around the Equestria, which caused spontaneous magical outbursts in unicorns"

"And since alicorns are part unicorn they are affected as well" The Doctor now had the jist of it yet he just needed a cure.

"Correct, it is recoverable so this is only temporary, but the magical outbursts will destroy canterlot before she can recover" The Doctor needed a place where she could heal without causing too much damage.

"I know a place where she can heal but it can't get here, so I need to carry her" the princess shook her head in disagreement.

"You wouldn't make it, the outburst at full power are too much for anypony, you would not survive, I can barely, keep the blasts suppressed. But I have something that could help" using the same technique she brought the book with, she had now brought a bottle of green liquid "this will dull the effects of the fever but It lengthens the time of recovery" The Doctor took the vial then gave it to Luna.

"Luna?" The Doctor tried to get the attention of the weak princess, not opening her eyes or speaking but stirring as a response "please drink this, it will dull the illness so I can treat you better" hearing his voice, told Luna that she was safe proving so as she slowly opened her mouth and drank the contents of the Vail, followed by a nasty cough "that bad huh?" the taste gone from her mouth she returned to her slumber with a gentle smile on her face at his humorous comment while also regaining some of her colour "Celestia" The Doctor asked in his serious dark tone that he had used against Luna as Nightmare moon during their battle while getting up from Luna's side.

"Yes?" the princess, heard about this pony from her student, about his dark atmosphere that she heard even her sister was scared of, and she could see why.

"I need, my element of harmony, with it I have the full abilities of an Alicorn so I can teleport her" following his instruction she left to open a vault which only she could open and she returned with the element of trust.

"Here is the element, please bring her home safe" The Doctor packed his bag and placed the element on his head, making him look like an alicorns with the helmet on.

"I promise, she will be fine…tell the others I'll be back" harnessing the powers of the element The Doctor attempted a spell that Twilight had shown him, a transportation spell, focusing on the library he noticed something else, it was everywhere, the same thing everywhere at once and only one thing was like that "Avanti!" and in an instant both Luna and The Doctor vanished and Celestia left to assist her subjects.

**At the TARDIS**

In a flash of light, both the ill princess and the time traveller, where now in a large room with a six panelled console in the middle of a platform which was raised above the floor The Doctor stood on.

"I knew it, only the tardis could be everywhere at once, now to the zero room" his little excitement over, he used his magic to lift the princess on his back and moved in the direction of the zero room. The zero room was a very special room meant for meditation and healing, just being here would heal most injuries in half the time, but infection would be healed in even less "here we are, been a long while since I visited here" The Doctor had set up a bed in this room since he liked to sleep in here every now and again, it was incredibly beautiful as it was modelled to look like a garden on Gallifrey. Now placing Luna on the bed, he took off his helmet and placed it on a table, which Luna would recognise when she woke up, exiting the zero room he turned a dial near the door which moved the sun in the zero room over the horizon bringing out the moon and The Doctor noted that Luna's mane had become more majestic in the moon light, he had never actually seen Luna at night "sleep well Luna". Now making his way out of his ship and out Twilights library he spread his wing ready to make a return trip to canterlot, his bandages also fell off as being in the zero room healed them quicker than even he could naturally do. Taking off, he raced towards the capital to assist in any way and he flew, in fact he flew so fast he made it in half the time.

**AT CANTERLOT**

The mane six and Celestia with many others were helping free the ponies from collapsed buildings and rushed them to hospital, but in the process rainbow burnt her wing while saving several people from a burning building, but she then noticed something flying very fast in the distance.

"Wait, who is that?" curious to who could fly that fast, a crash could be heard and turning round, she saw the castle tower had lost it integrity and had broken off. Closing in was The Doctor hell-bent on saving lives and below the falling tower was the hospital, knowing that there was no time, he lowered his altitude and aimed for the hospital, his friends saw their friend race to his target and just has he reached the wall…it happened, he had flown so fast he had reached and surpassed the sound barrier, but instead of the Sonic Rainboom even a regular sonic boom, there was nothing his body became engulfed, in electric energy that when he passes the wall …there was nothing, no Doctor, but on the ground was a trail of flames along the straight road, everyone stared at the trail left behind by the time travelling pony, and looked to the imminent fate of the patients at the hospital. However by The Doctor's view everything had slowed down, he saw the flames on buildings burning slow, the noise deeper and longer _"I did it I broke the sound barrier, but not in the way I pictured it" _taking advantage to his new ability, he flew past homes, the market and several ponies on the street all while leaving a strong gust of wind behind him in real time to everyone else. Reaching the hospital he flew in the window and grabbed as many as he could and moved them to a safe area, taking all the time he could, he made several return trips finally, only several children remained, grabbing them and flew to place them with the nurses who had moved to find themselves in the garden but still moved to slow by the doctors point of view, now the rescue op complete he flew to his friends using his wing as air breaks to slowdown, upon a sudden drop in speed, his hooves caught the ground, and made the same flaming trail he had started with. All his friends including Celestia were shocked to find that he had just saved thousands of lives in less than couple of seconds, even rainbow could not believe it but in the same second she saw the burning trail the first time, the large population of the hospital was in the garden.

"How did you do that?" was The Doctor's best friend Twilights question that everyone wanted to hear.

"I broke the sound barrier, you see ever since I arrived in this world, I have been practicing flying, and since I had no idea how to, I based my movements off Rainbow and in about a month I had learned how to fly and every week I timed myself going round and round, ponyville, my time getting quicker and quicker, the reason I didn't get here sooner in the first place was because I was injured and I wouldn't leave Rainbow behind, so when I dropped off Luna, I unleashed my full speed and made it here, but when I was trying to break the sound barrier, I crashed and hurt myself several times, but I was so focused on helping people, when I saw the falling tower it just clicked and next thing I know is that I'm flying at normal speed and everything was moving at a thousandth of a second, so I rescued everyone in several minutes by my point of view but by yours I was literally a split second, cool huh?" he explained looking like a very happy puppy, near the end of his explanation. looking back he saw the flaming trail he made "oh my God, that's what happens when I travel the sound barrier, oh that is just smashing, I'm like a de'loren on hooves" everyone was shocked that he was actually faster than Rainbow, she herself was trying to calculate it in her head, she was flying at her full speed without trying to use the sonic rainboom, surprised that the doctor could keep up, but he was faster all along and it was only his injury's that slowed him down.

"Hold up! How can you be faster than me?" Rainbow stated with anger and annoyance with The Doctor and as usual he was lost and confused at her question "well speak up" now with her face in The Doc's it was now more difficult to explain himself.

"_Bugger, what do I do now" _thinking off a strategy that could get Rainbow of his back "it's because I am more mature"

"What is that supost to mean?" she began to raise her voice even more.

"It means that I can roughly travel at the same speed may be slightly faster than you because I'm older and my wing's are more developed! In my world people don't usually fly naturally so machines were made to allow flight, in the development were scientific ways to gain altitude and momentum and since you ponies never needed artificial flight you never thought of different flight techniques! It's the reason I lost altitude before passing the wall as gravity would of allowed me to fly faster but I didn't could on breaking the sound barrier!" The Doctor now talking serious as to force Rainbow to back down "don't you see, you are an incredible flyer and will have more experience than I will for quite some time, but my own experiences and ability to think outside the box in terms like this will allow me to surpass you, plus your only 16, I'm over 400 and my body is technically still a Time Lord so my body is developed accordingly probably which is why my wings are more like an alicorns than a Pegasus. So I'm sorry Rainbow but the fact I'm faster can't be helped" rainbow now saddened by his explanation walked off with her head down.

"Yea I guess your right" as the other five of their friends along with Celestia stood watching The Doctor deal with Rainbow, the time lord walked over to her and past her without looking at her.

"But remember this Rainbow Dash, no matter how fast I fly or if I beat you in a race I will never be the fastest pony in Equestria" Rainbow regained some integrity and wondered what her strange friend meant "it because I don't want to be, I was the best on my world, I could match anyone in math, science, engineering, I could of become the most famous Time Lord of my time but I decided to become a teacher and my life was defined by war and then loss followed by the drive to explore and discover. Why I'm here I have no clue but why you're here is crystal clear, you have the power to define yourself though your talents like every pony else, but my talent is not fixed, now I've explained myself, Rainbow are you going to let that stop you from becoming the greatest" looking up from the ground an into the Ancient eyes of her friend from another world she raised and shook her head.

"No I will be the best, sorry for getting mad at you Doc" putting a smile on his face, one question that only the doctor could answer was in the princess's mind.

"Doctor, my sister is she safe?" The Doctor turned to his friends mentor to give her some good news.

"She is fine as soon as the potion we gave her wares off my Ship will keep her energy contained and protect her from harm" the mane six were still puzzled to the cause of the developments that they still had questions.

"Doctor, what was wrong with Princess Luna?" Twilight ask as he finished reassuring Celestia.

"Luna was the victim to a virus, that affects unicorn magic and being an alicorn is no exception as it seems to affect magic directly, she is right now in my Ship recovering with the help of some of my native technology" now informed the 6 headed to the damaged palace in order to discuss the repairs of Canterlot, The Doctor was about to follow but not before clearing some facts to the crowed that had followed the flaming trail he had left behind "Citizens of Canterlot!, this event was an accident and no one is to blame, now that the crisis is over I ask you to assist in the recovery of the city and to never speak of this day again and to show I am serious" the doctor brought out his sonic screwdriver making the public wonder what the device was, after activating it every camera in the area was destroyed along with any pictures concerning the day that had past "your cameras are destroyed to prevent photographic evidence and if I find one article even one sentence of what happened here I will make sure you lose everything and trust me when I say I have the power to do so!" now walking away from the crowd which was shocked at how this one pony could address the public with such a calm and frightening voice and demand their silence.

"Thank you for protecting Luna" Celestia gave The Doctor her gratitude as if Luna found out she had done this it would leave her heart broken.

"She doesn't deserve to live her second chance in the fear of being feared by others" the doctor walked to the wall surrounding the city and spread his wing ready for the flight back "I'm going to check on Luna, I'll be back" showing his incredible speed he shot off in the direction of ponyville and in mere minutes landed (rather badly) in front of Twilights house, leaving a descent sized crater at the door "oww, that hurt, it seems I need to work on that landing" now racing into the TARDIS he entered the zero room to see Luna sleeping peacefully now with her colour fully returned "thanks old girl for taking care of her" the TARDIS discreet humming changed tone as a response to it lifelong owner and friend.

Returning from canterlot the mane 6 returned to their homes and ready to go back to daily life's, however The Doctor never came back with Luna causing Celestia to worry more and more asking twilight to check on her upon her return and she was definitely surprised to say the least, before opening her front door Twilight could hear laughter opening the door she saw on the couch the Princess and The Doctor laughing their faces off and in the chaos The Doctor noticed his purple friend at the door (after falling off the couch of course).

"Twilight I was just telling Luna about the time that I crashed onto a snow covered planet and in the process angered a Hugh Bear like beast and ran away nearly wetting myself in the process" continuing with the laughter Twilight giggled a little herself happy that the princess was well again.

"Well I just came to say that Celestia is still a bit worried it would make sense to release her of the stress" getting up from the couch Luna walked over to twilight and to the door with a happy smile on her face.

"Yea I suppose you're right, I mean I would also be worried if Celestia was hit by the debris instead of me. It just sad that I could not help any pony else during the earthquake" Twilight was confused there was no earthquake, was it possible she is suffering from amnesia from the affects of the virus "thank you again Doctor you have been a great help" giving off a small wave and a smile The Doctor said his goodbyes and Luna disappeared using her magic.

"Doctor, does she not remember" The Doctor still with a small smile shook his head as an answer to his friends question.

"No, before she woke up I wiped all memory of the incident from her mind and explained when she woke up that an earthquake had struck causing the structure of the Castle to break apart and she was hit by debris after helping save a couple of ponies, I also sent a letter just a few minutes ago to Celestia to never speak of it again, she should be done explaining it to her subjects now" Twilight's relive was turned to anger as The Doctor had messed with someone's memories without permission and (as she though) experience in doing so .

"Doctor that was reckless!" now confused The Doctor got up himself not knowing what Twilight was on about.

"What was?" he said cocking his head a bit.

"You can't just use the elements of harmony play with someone's memories like that and you may be able to fly perfectly now but you still know little about magic especially alicorn, you could of seriously damaged her mind" Twilight had believed that The Doctor had used the element of harmony that gave him the power of an alicorn to alter Luna's memory but she was the one at fault and The Doctor's atmosphere was dulled once again like it did when Rainbow confronted him about his ability to fly.

"Yes, your right I don't know much about alicorns but I didn't use the Element" Twilight and The Doctor were prone to argue but over little things, this was a battle that had never been considered.

"What do you mean by that?" Twilight asked wanting to see what kind of explanation her lodger could give.

"This isn't the first time I've altered someone's memory and I didn't use the element because I didn't use magic and I know a lot more about the mind than you do Twilight's if you want to continue arguing about the method then listen to the reason!, she lived for 1000 years alone and upon her return she was feared and when we stopped her dark side and brought Luna back she was still afraid and alone, imagine if she knew she was the cause even unintentionally of the events that have occurred today" Twilight now could see where he was going and felt sorry for doubting her best friend.

"I…I, She" as she too like Rainbow was beginning to tear up over her misjudgement The Doctor walked over and hugged the Purple unicorn.

"She would feel even more detached and lonely, we are her only friends and even still we don't see her that often, did you see her face when you walked thought that door, that was probably the first time she laughed that hard for a millennia and I forgive you Twi for questioning my actions as you were also concerned for her health, but let's just be glad that she is now happy that she has friends that she can rely on ok" now braking off from the hug The doctor dried off some of Twilight's tears and Spike walked in not knowing what was going on.

"Hey guys, what I miss"

Next Time:

Trixie: I am the great and powerful Trixie and anything you can do I can do 3 times better

Doctor: bet you can't go back in time and say hello to your self

Future Doctor: Yea, that I'll be the day

Apple Jack: Sweet Celestia there's two of them

**GREAT AND POWERFUL TRIXIE VS THE LAST SON OF GALLIFREY**

**COURIER**: I found this chapter very good, please review and give me any feedback on what could be improved or about your thoughts on episode 4. Any way thanks and have fun you guys

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	5. Episode 5: The Doctor Vs Trixie

COURIER: episode five, the battle that will shape the very fabric of time and space…

This episode will not include the big bear but instead a duel of tricks and wits, HAPPY PONY GAMES AND MAY HARMONY BE EVER IN YOU FAVOR…ooh that's a really good idea

Disclaimer: I do not own Doctor who or MLP: FIM

Doctor Who:

The Equestrian Chronicles

Episode 5:

_**THE DOCTOR VS THE GREAT AND POWERFUL TRIXIE!**_

"Come on Twi" The Doctor along with spike were urging on Twilight as she practiced her magic, The Doctor usually works on the TARDIS but some of Twilights tricks sparked his interest and volunteered as attest subject along with spike

"You can do it" the little dragon also urging his owner and friend

"Ok here goes" as Twilight reassured herself she charged up her magic and unleashed it on the Time Pegasus and dragon causing moustaches on both of them

"Ha ha you did it!" spike congratulated twilight on a successful test while The Doctor was…

_(LIGHING AND THUNDER AND EVIL MASTERMIND MUSIC IN THE BACK GROUND)_

"MU HAHA, I the great and powerful Doctor Rassilon will rule all of Equestria as the pony Lord of Time" Spike and Twilight wondered how the music and lights happened and both thought he was planning this from the beginning

"Sorry Doctor, it's just for practice and it's got to go" Twilight deactivated the spell causing Spike the Doctor's moustache to disappear as well as the effects puzzling both of The Doctors roommates once again

"Aww, I looked epic, in fact it reminded me of my godfathers moustache when I met him, dam he was a lot of trouble, I think he's reformed and scarified himself near the end of my dad's 10th regeneration, he never explained the details" The Doctor explained before leaving the library with his two friends

**IN THE TOWN CENTER**

Both The Doctor and Twilight were strolling in the Equestrian sun, discussing different topic they've been working on

"Still 25 tricks and counting, you're developing quite the arsenal" The Doctor was writing in his note book (using a device that held his notepad and embarrassingly asked the ponyville school teacher Miss Cheerilee to help him write with his mouth)

"You think, I think it's great practice" Twilight said with her usual smile. As the two ponies enjoyed the hot sunny day and continued walking yet just at that moment two more slightly younger ponies ran past and somehow dragging The Doctor with them

"Ahh, hey! Let go!" The Doctor screamed trying to use his wing but before he could they stopped causing The Doctor to go flying and crashing into the side of a house "logic! You traitor" he stated as he got up and dusted himself of "all right You two! start talking"

The two known as snips and snails (why someone would call their son snails I have no idea) both looked extremely happy and where heading for the town square "haven't you heard, there is a new unicorn in town!" snails explained like it was common knowledge

"Yea, they say she's got more magical powers than any other unicorn ever" snips also explained while jumping up and down

"Well unless her special talent is magic with a side dish of ketchup, I don't think she could match up to someone like Twilight or me for that matter" he said in a calm and controlled voice unlike the other two

"Well you'll have to see for yourself come on" snail explained and both raced to the square with both The Doctor and Twilight in tow

**TOWN SQUARE**

Nearly the whole town was gathered in the town square to witness the power of the unicorn known as Trixie

"COME ONE, COME ALL WITNESS THE INCREDIBLE MAGIC OF THE GREAT AND POWERFUL TRIXIE" she announced herself while rolling the R in her name and the little shack in front of the crowd had opened up in to a stage and she appeared out of smoke "watch in awe as the great and powerful Trixie performs the most spectacular feats of magic ever witnessed by pony eyes" this time exaggerating her words with fire works

"my, my, my, what boasting" the fine example of Rarity gives her comments as she details that Trixie is showing off, with spike also sharing her opinion

"come on, no pony is as magical as Twilighiiii…" spike instantly realising who he was standing next too. The Doctor had discovered on his second day as a pony that spike had a massive crush on Rarity which he thought was weird since they are both different spices but he could recall from experience if you live with a species long enough you can the attraction "hey Rarity…moustache!" he exclaimed before dashing off confusing Rarity in the process

"Nothing's wrong with being talented is there" Twilight asked since she was clearly talented and was worrying about her friends reactions to Trixie

"Nothing at all, except when someone goes around showing it off like a school filly with fancy new ribbons

"I'm going to pretend I understood that Apple" The Doctor said since he was oblivious to most of the metaphors AppleJ used

"well that's your problem, mister smarty hooves" Apple responded with her strong Texan accent

"Just because that one has the ability to perform lots of magic does not make one better than everyone else" Rarity explains and pretty well

"Especially if you got me around being better than everyone else" Rainbows statement bought a death glare from both Time lord and farmer "I mean magic's shmagic boo" she tried to correct herself as not to face the wrath of the two together, however this discussion caught the attention of Trixie who was one to protect her reputation

"it seems we have some NEIGH-say'ers in the audience" the instance that she did that The Doctor heard uncontrollable laughter in the back of the crowd, he too found Trixie's cliché horse sound hilarious but unlike the brown stallion with the green tie at the back he controlled his amusement but still gave a smirk "who is so ignorant as to challenge the magical ability of the great and powerful Trixie, do they not know that they are in the presence of the most powerful unicorn of all of Equestria"

"Pffft, cheap parlour tricks combined with real magic, that's nothing special" The Doctor could take from experience he had met some of the most famous magicians in his universe "she's a 2nd grade magician at most" however Rainbow never backed down from a challenge

"So great and powerful Trixie what makes you think you're so awesome anyway" rainbow using her 'not loud at all' sort of touch

"Only the great and powerful Trixie has the power to fend off the great URSA MAJOR"

"I would like her reaction to a weeping angle, the cocky witch" The Doctor was known for insulting people for little reason but Twilight had no idea what a weeping angle was and knowing The Doctors she didn't want to know

"it is true Trixie is most certainly the best in ponyville" it seemed that Trixie would continue boasting and wanted to show off her talent "don't believe the great and powerful Trixie" she said in on second long shot "well then i herby challenge you ponies of ponyville anything you can do I can do better" the thought rushed through every one of the mane 6's head to put her in her place and of course one was bound to stand up "or is Trixie destined to be the greatest equine who has every lived" Spike who had his mouth zipped for some reason was begging Twilight to outshine her but that was before Trixie challenged Twilight herself but after a bit of hesitation it turns out she was talking to Apple jack

"That's it, I can stand no more of this" she announced walking up the stage and she began to show a little of her talent "can your little magic do this" and of course she was amazing as she was doing robe skipping near perfectly with the rope bound to her tail and than using the rope to pick an apple which landed perfectly in her mouth "top that missy" and of course Trixie had a trick up her hat

"oh ye of little talent watch and be amazed at the magic of Trixie" and taking off her hat to use her horn she possessed the rope like a snake which actually mesmerised AppleJ and went off to pick an apple before tripping and binding her legs together and stuffing the apple in her mouth like a pork amazing the crowd after rainbow also tried and failed to win followed by the embarrassment of Rarity, this was the last straw

"Ok that's it this has gone on long enough" The Doctor stood up onto the stage and was ready to put Trixie in his place

"And what can you do that the great and powerful Trixie can't" she said with confidence unknown of the Pegasus which she enraged

"Bet you can't go back in time and say hello to yourself" not many ponies knew The Doctor but he was good at what he did second to none

"That would be the day" and like that another pony walked from behind the curtain wearing the same Tartan tie and same colour mane and coat, in fact looking closely it was the same pony, there were two Doctors

"Sweet Celestia there's two of them" Apple jack said in shock, both Doctors stood like one looking in a mirror and both looking at Trixie who was shocked to say the least

"So what, using your twin isn't magic" the suppose future Doctor smiled while looking at the present Doctor

"Do you want to show her or should I" the Future Doctor asked his past self

"Nah be my guest" the Current doctor said with a calm voice "oh did you bring it?" and upon asked the future doctor brought out a leather watch looking thing and pressed a couple of buttons "see you when I'm you" and with one final press the current Doctor vanished leaving the future Doctor in his place and it was clear that the doctor didn't vanish in smoke or magical energy in fact it seemed electrical and a smoke mark was left in his place

"Hello future me or I'm present me now, oh and Trixie here" the now current Doctor gave Trixie a pile of photos which were in fact foal pictures of different ponies including herself and each picture had the doctor in it even Celestia was in the collection as the bright pick mane and the pure white coat was unmistakable

"how is that possible, you can't still be the same taking these photos you should be old" she stated dropping the photos revealing them to the crowd, but the doctor picked up the Celestia one as she wouldn't appreciate her Foal photo in the paper

"Time travel, you should try it sometime, now where did that Luna one go?" seeing as she couldn't top that she resorted to a different tactic and did a similar bind to the doctor that she did to Apple minus the apple

"Seems even you can't beat me even with your impressive talents" but the doctor was back on his feat quicker than she seemed possible

"met Houdini learnt his tricks, binds are like cake" and for some reason the Doctor was now wearing a Fedora which some of the mares screamed as he looked rather dashing and Trixie was losing her edge "here let me take your cape" flinging a small pellet to the ground the entire stage was in smoke and once it cleared there were 3 Doctors all wearing a tartan tie and different hats on with a fedora, one with a top hat and one wearing a fez and all three were holding a copy of her hoof woven cape which she still had on

"How is, how is there three of you!" Trixie was now a bit dizzy as even she couldn't comprehend how three could appear and be completely identical "triplets? It has to be!" but her theories where shot as yet another Doctor appeared from the crowd

"Sorry Trixie, I don't have any brothers, I do have sisters though" and again another

"Hey! So do I!" and one by one, more and more doctors showed up all with their eyes on Trixie who was more nervous than Fluttershy on a bad day. And one stepped forward wearing a tartan bowtie and sporting a smashing moustache

"Great and powerful Trixie! Meet your defeat at the hands of Doctor Rassilon! muhahaha!" but this one was shot down by the fedora wearing Doctor with a baseball bat

"You weren't suppose to show up you old coot now scat" Doctor Rassilon sulking away and the Fedora Doctor turned to face his opponent "it seems I win" now completely freaked Trixie backed off afraid of the Time lord, Twilight did a quick count and saw 24 Doctors in all "see, even you can be stopped in your tracks and I didn't use an spark of magic, in fact most of your tricks are just for show, like what you did to Rarity, just a combo of green hair spray and some mud, and it's not difficult to spin rainbow out of control she does that enough herself"

"Yea! wait what?" Rainbow a bit confused at The Doctors statements

"but this is magic" taking of his hat and his Sonic screwdriver while standing on his hind legs, he tapped his hat three times and pulled out Spike, how he got there no one knew, Gummy (Pinkies pet alligator) and then he struggled to get the last one out, he hit his hat a couple of times even letting one of his other self's try but eventually to the surprise of every one, Trixie especially and the person who came out of the hat was in fact princess Celestia

"oh heavens, where am I" looking around she saw her student Twilight and her friends along with the rest of ponyville which had bowed after about two minutes of shock, finally looking behind her she saw the legion of Doctors "oh hello Doc…tors, do you mind explaining to me what just happened?" after asking her question The Doctor gave a bow (in the thank you kind of sense)

"Princess, a magician must never reveal his secrets, now back to canterlot with you" placing the fedora on Celestia's head and tapping it with his screwdriver three times again the princess was warped back into the hat with the Doctor replacing it on his head "ta da"

Now defeated, Trixie backed off "you may have defeated me Doctor, but you haven't seen the last of THE GREAT AND POWERFUL TRIXIE" flinging a smoke pellet, not at the same strength as The Doctors, to the floor Trixie could be seen fleeing and faint in the back ground was the sound of her vowing her revenge followed by screaming

"and my work here is done" with the entire crowd cheering thinking it was special effects every doctor used the same device the first one used and zapped out of existence. The mane six where proud and astonished at the skill of their friend, but like all magicians he had one last trick up his sleeve

"That was amazing, don't you think Twi!" sitting next to Twilight and eating popcorn was The Doctor with no hat or moustache and Gummy with his jaws snapped to his mane but realising that he was there the whole time made everyone jump

"How in the hay did you do all that?" Apple jack asked the grey Pegasus of time who was still eating popcorn

"I remembered I still had this vortex manipulator in my room, so by using the power of probability I decided to get it later on and give it to myself in the past while in the process visited myself over 20 times" he said showing off the device "I wouldn't of done anything but what she did to you three was just plain cruel so I had to reveal her flaws. Oh and pinkie this little guys yours" he said giving Gummy back to pinkie who jumped off in excitement but The Doctor had one more thing to take care of "Twilight right now I should be back at the house but I need you to give me number 25" rearranging his tie to a bowtie Twilight giggled and gave The Doctor a moustache turning him into Doctor Rassilon and using his Vortex manipulator he vanished

**BACK AT TWILIGHTS HOUSE**

In a flash of light the Doctor walked through the door to catch Twilight writing a letter to Celestia and spike with his own moustache sulking about a failed attempt to woo Rarity

"You're late you know!" Twilight said with a mischievous smile on her face and in a second the doctors fine moustache had become a large white beard as punishment for his lateness, but as Twilight learned that day, never ever give the Doctor Facial hair

_(Blue pointy hat appears on The Doctor head and a staff in his right hoof)_

"A Time Lord is never late not is he early, he arrives precisely when he means to" making both his Companions laugh uncontrollably

Next Time:

First Date (Sorta)

Courier: now, now, don't worry if you weren't satisfied, if you have seen the show a more epic battle will boil between these too foes , but for now back to the Story arc!

Doctor: Can I tell them? Can I? Can i?

Courier: no! _**"Reveals baseball bat of omega"**_(a most powerful weapon which can only be wielded by god himself of this world 'by Princess Celestia') BATTER UP!

Doctor: DOCTOR WHO IS BALSTING OFF AGAIN!

Courier: what he was trying to say was that Episode five will and I stress the WILL involve _**"in a godly voice, complete with lightning and thunder**_" TIME TRAVEL!

So guess what the episode will be like, I may have left a clue in any of the chapters, as by the time I've written this I'll go to sleep with it on my mind.

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	6. Episode 6: First Date (Sorta)

Doctor Who:

The Equestrian Chronicles

Episode 6:

First Date (Sorta)

**Black Hole Prison (The most secure prison in Equestria)**

Far in the future, by request of a certain hero a prison was built to contain the most dangerous criminals, but even after 30 years only 12 prisoners were ever sentenced here, one was so familiar it reminded the inmates of who built this hell.

"Well, well, well look who we have here" a black Pegasus stood in front of the cell of the most dangerous Criminal in Equestrian history, the criminal in question was a Pegasus but he hid in the light so all the black Pegasus could see was the scar on his left eye accompanied with the hatred that kept him alive for the entire live of the prison he was in, he was Prisoner Zero.

"What do you want" he said in a voice that would cause the prison to go berserk if they heard him on the bottom floor.

"I want to make you a deal, i want you to help me remove your doppelganger from the picture, permanently" the Dark Pegasus stood with elegance and might and spoke with a cold but calm voice.

"HA! He is no doubt the most powerful being in this s*** hole of a world" Zero laughed manically as the dark Pegasus knew he needed convincing.

"Yes but he isn't the most powerful, that goes to his daughter" the news shocked Zero as he knew very little about the outside world the past 30 years.

"A daughter!? I thought Time Lords were sterile"

"He solved the problem years ago, the wedding you attempted to use to ruin his live just fuelled his love for the bride, they have had two children a son and daughter, both extremely powerful, but the girl was born an alicorn and has enough magical energy that her power is equivalent to the Elements of harmony, hence her name" now informed about the family Zeros nemesis has made he wondered what this mysterious Stallion had in mind.

"What's in it for me? Freedom won't do it i only have one live left and i will need to regenerate to stand a chance and i can't risk losing if i can't survive because he WILL kill me if he finds out who i am" Zero asked and explained while standing.

"I can give you a new cycle, and the means to take him out, so do we have a deal?" the dark Pegasus asked with a smirk on his face.

"Two conditions, how do i take him down and who are you?" unlocking the cell freeing Zero, the dark Pegasus walked away from the cell heading for a black box which looked like an elevator, standing next to the box was a beautiful grey earth pony with black hair,opening the door to the black box revealed a large room just out of Zeros view "a TARDIS!"

"How you take him out i'll leave to your discretion as for my identity you can call me The Valeyard" as he said his words the box doors slid shut and the Black TARDIS disappeared like all the rest but its sound was broken like it was as twisted as its pilot but on the floor was a note and a watch like device and a vial of golden energy, the note read.

_Don't look for me, ill find you, Professor_

_ The Valeyard_

"Well then, its time to pay a visit to my Doctor"

**PRESENT DAY, ONBOARD THE TARDIS**

They mane six where currently at rarity's to get ready for the Gala, The Doctor told them he would meet them there as he was taking the TARDIS, he was currently in his wardrobe trying on the TARDIS blue suit Rarity had made for him, even the TARDIS made the Pockets bigger, he was looking at himself in the mirror.

"I look like my father just missing the spiky hair and the brown coat…ignoring the fact I'm a pony" after ogling himself he walked back to the console room and set the controls to Canterlot.

VWROP, VWROP, VWROP

**CANTERLOT CASTLE**

As the TARDIS landed near the Canterlot gate, The Doctor stepped out in his dashing suit turning the heads of a few mares, reaching the main gate two guards stood to check tickets.

"Excuse me sir but unless you have a VIP ticket you'll have to wait in line" looking as the guard with a smirk on his face he pulled out his Gala ticket which was signed by Celestia herself "my apologies sir i had no idea"

"No worries my good man just doing your job, here is a little something" giving the guard a gem, passed him and into the palace to look around, after a good sweep of the ground floor he came to the grand stair case with Celestia and Twilight greeting the guests that came to the gala.

"Doctor!" Twilight greeted The Doctor as he walked up the stairs.

"I am glad you could make it Doctor, Luna will be glad to have a friend to spend the night with" Celestia said with her usual elegance.

"Well i got to say and no offence, it looks pretty boring, please Celestia let me arrange things next year" Celestia gave a small giggle and nodded in confirmation "of course Luna is in her room" she raised her hoof to signal a guard, who was a white unicorn with a blue mane similar style to Twilight's.

"Hi Twily" he greeted his sister first as he had not seen her since she moved to ponyville.

"Shining Armour, its great to see you BBBFF" of course the phrase BBBFF stumped The Doctor making Twilight role her eyes at her alien best friend "Big Brother Best Friend Forever" she explained.

"Oh, fair enough, nice to meet you Shining Armour" The Doctor greeted the captain of the royal guard him giving a nod and turning his attention to Celestia.

"Princess what is it you require?" he asked the princess in a casual manner, most soldiers no matter what rank would address royalty with the upmost respect but this captain was calm and relaxed this as another example of Celestia's rule, she ruled with care and kindness.

"I would like you to escort The Doctor to meet my sister" according to Twilight she never gave an actual order, instead she asked more often but ether because she is so kind and polite or because of her position no one will say no, even if they did she would forgive them and sort the issue out.

"Of course Princess, Princess Luna's Room is this way" he addressed The Doctor and both left the presence of the Princess and her gifted student "bye Twily, i'll see you soon" Shining Armour waved good bye to his little sister before walking off

"Remember to have fun Twi, but don't do anything i would do...in fact i should of told that to pinkie but oh well" The Doctor also said goodbye to his dear friend as her only brother escorted him to the reason he came here in the first place.

"Bye you guys and i will, see you soon BBBFF and don't cause a stir Doctor" Twilight said as both Pegasus and Unicorn left the main hall.

**CANTERLOT CASTLE CORRIDORS**

As both stallions walked the halls, Shining Armour was thinking about this colt that he had to escort.

"_Who is this guy, Twilight has never mentioned him unlike her other friends, the way he talked to her, it was almost like the way we talk to each other, this pony better not be involved with my sister in any way other than friends"_ Shining was being the cliché Brother concerned about the friends his sister makes "so how did you meet my sister?" Shining asked trying to get as much info as he could about the grey coated Pegasus.

"Its a long story, but to dull it down in the shortest sense, i crashed in to her house and ever since she was kind enough to let me stay" that was the most odd way a guy ever met a girl making Shining eyes widen.

"So Mr Armour was Twi always as paranoid as the way i know ..." before he could finish his sentence Shining pulled out his Sword and pointed it at The Doctor who just stared at it and back to Shining like it was a normal occurrence.

"Let me get something straight, you better not have any funny ideas about my sister and if you ever hurt her in any way i will hunt you down and kill you my self" as both stallions stared at each other for what seemed like hours, The Doctor raised his hoof to lower Shining's sword.

"Listen Shining, i do not like your sister in that sense, i am a lot older than i look so for me that would seem just wrong" he explained giving a shiver "plus in the time i've known her i see her the same way you do, as a sister and nothing more" now understanding where The Doctors loyalties laid, he sheathed his sword and turned around.

"Ok, I trust you but i stand by my word if you hurt her" he spoke with darkness in his voice, to which the loon that was The Doctor gave a salute and both continued to walk to Luna's room _"i want to know why Luna wants to see him of all people, he's a complete nut but Twily seems to trust him, so ill let it slide"_

Arriving at a large door marked with the symbol of the moon, Shining gave a small knock followed by a young female voice "enter" opening the door both shining and The Doctor saw Princess Luna at her window watching the moon and the party below.

"Princess Luna, you have a visitor" turning her head to the door she saw The Doctor standing with a small smirk on his face, Luna had changed her look making her mane longer and transparent like her sisters, Shining had seen her like this plenty of times before but The Doctor only saw her like this once and she was asleep and ill at the time not to mention she was in probably the best designed dress in Equestria and The Doctors reaction was priceless.

_*Pomf*_

It seemed that only The Doctor noticed it happening and he quickly brought his wings down but couldn't fold them.

"_Bloody wings why are you being awkward now!" _he thought to himself with mental sweat pouring down his face.

"DOCTOR! it is so wonderful to see thou could come" Luna shouted (no royal voice, still pretty loud) then she ran over to him and gave him a hug, returning the hug The Doctor saw Shining smirking trying hard not to burst out laughing and The Doctor had no clue what Shining found so funny, till he saw one of his wings sticking up.

"_Dam it wings!, i'm going to cut you off and feed you to a dragon" _The Doctors mental rage against his wings put his mind off Luna and his wings lowered, which made The Doctor think _"wait was i just aroused?...how odd"_ after Luna broke the hug The Doctor tried not to be distracted by the attraction he was having for Luna, an attraction he couldn't understand "its good to see you Luna, how have you been?" he said caringly.

"Not the best, in fact thy duties haven't really changed since i last performed them" Shining left the room closing the door behind him and letting the two chat each other to death.

**TWO HOURS LATER (AND A LONG EXPLINATION)**

Both Alicorn and Pegasus sat side by side on the balcony, enjoying the Night sky as both The Doctor and Luna's talents had some thing to do with the stars.

"So thou change your appearance when thou are close to death?" The Doctor had just finished explaining where he came from and how he looks like he is and had just explained regeneration.

"Yea, that's pretty much the jist of it, the thing is i don't know if it will happen next time, this world is so different but i will probably still live my natural live span, so at least i can live knowing two of my friends won't die of old age" he explained everything in a cheery mood and Luna knew that it was all for show, she knew that the thought of this regeneration frightened him, living for 1000 years was bad enough but having to change your entire body, it must of been horrifying.

"We never knew what it felt to outlive friends and loved ones, as we didn't have any" Luna was now depressed as she remembered her lonely childhood, her only friend being Celestia but after time had been to busy with her new royal duties to play with her.

"Least you had a childhood, i joined the Time Lord academy at the age of eight and for the next ninety-two years i did nothing but learn, then after that the war started" Luna was again shocked that both had shared similar childhoods but he did not hear the last part and before she could ask The Doctors spirit sparked once again "also what's with the thou and the we?" Luna was a bit confused as no one commented on the way she spoke before but then again she had only been back 4 months.

"It is the royal we and this is how thy speakest" The Doctors eyes spoke for him and he knew something had to be done about that.

"Well i think we need to twitch that i tiny bit" he said pulling out a Canterlot dictionary and Luna's eyes went wide with horror _"oh no, not school"_

**THREE HOURS LATER AND AN UNWILLING STUDENT**

"Ok now repeat the sentence" The Doctor said pointing a metal stick to a chalk board with some writing on it.

"Hello my name is Luna and i am the Equestrian princess of the night, i have an older sister named Celestia... Doctor this is a Childs lesson, you don't have any reason to tell me how to speak, i don't even need it" Luna had sat on her bed listening to The Doctor for three straight hours and she was sick of it.

"Huzzah, not the sentence i made but you used modern words! And let me say from personal experience that speaking like you did just confuses people but still your done" he said pressing a button on the chalk board which made it fold up to fit in The Doctors pocket, Luna on the other had was confused she was now speaking more modern and it was a strange experience for her.

"Oh your right i am speaking like a normal pony, oh this is spectacular" she exclaimed with so much joy.

"Well at least you have a large vocabulary" The Doctor said with sweat dropping down his face as a reaction to Luna's excitement, then he felt a small vibration in his pocket "huh?, what the?" pulling out his psychic paper, it flashed in a bright blue light which drew Luna's attention.

"Doctor, what is that?" Luna asked as she had never seen anything like The Doctors Psychic paper, in fact no pony has, it was a human wallet after all.

"it's called psychic paper, it allows the holder to fool the viewer to what they want to see but it can also be used as sort of E-mail system" he spoke with precision and concern at the thought of who could send him a message on Psychic paper "probably my step mother"

"What's an E-mail?"After asking her question The Doctor snapped his head to face Luna, then he relaxed after realising Luna had been on the moon the past 1000 years and that the only computer he knew of was the TARDIS monitor.

"Uhh, how to explain, ahh you know how you send letters to people" he said hoping that she will get the idea.

"Yes, why do you ask?" she spoke slowly as it was common knowledge.

"Well it's like that but electronically but never mind that now I need to read this" still unsure what the alien Pegasus was on about she walked behind him and while looking over his shoulder, read the note in his hand

_*****__**We need help, come quickly**_

_**From Harmony**__*****_

The Doctor looked up from the paper and directly at Luna, making her blush a bit since he was so close and both were in direct eye contact.

"Do you know a Harmony by any chance?" he asked cocking his head, which Luna found adorable giving a small giggle given the near awkward moment, yet she didn't have to think very hard about his question.

"My apologies Doctor, I do not" she said sad she couldn't help him out, but The Doctor jumped up onto the table with his face full of determination and a sense of purpose.

"Well then, we have no choice" he spoke with pride in his voice, Luna's heart was beating faster and she didn't know why.

"_Why is it getting hot in here? The window is wide open"_ The Doctor then leaped of the table and walked to the balcony ready to leap off the edge, "DOCTOR STOP!" Luna would have tried to stop him but she had forgotten that he could fly but before he jumped he turned to Luna with a massive grin on his face and his eyes sparkling in her moon.

"well come on then!" saying his words he fell backward off the balcony and soared off from the Gala and realising that there was nothing better to do, she ran for the window and she too took off into her domain of the night sky. Looking all over for the Time Lord Luna spotted him standing next to his Box once she landed she walked over to him slowly and she didn't look very happy "well that was fun wasn't it?"

"Doctor never do that you scared me to death!" she yelled whacking him on the head.

"Oww! HEY!" complaining about the growing bump on his head, the TARDIS door opened revealing the temple like room that resided inside and Luna nose up disapproval walked in first with The Doctor walking in after her.

"So where are we going anyway?" she asked still annoyed at The Doctor who could feel her cold heart a mile and a day away.

"well, a clever way to contact someone from the past is to send it to a place you know the receiver will be and the time they'll be there and this message is the opposite, it was sent from the future going back to point where the message was appropriate" he explained very quickly but like always he begins to ramble.

"That does not answer my question" she said coldly and in the background the TARDIS made some noises which to The Doctor's surprise Luna seemed to, like himself understand the old girl "huh? Who was that?"

"Wait you can hear her!" The Doctor said with shock in his voice.

"Hear who?" now confused with what was going on around her, she never spent long in the control room only a brief few minutes.

"The TARDIS, you can understand her!" he said with wonder as this has never happened before and along with his glee the TARDIS gave another series of sound which both The Doctor and Luna identified as a hello.

"Uhh, hello to you too…TARDIS, but any reason Doctor you still didn't answer my question" she asked once again.

"Ahh yes, well like a letter a psychic message has a sender and therefore an address" placing the psychic paper on what he called a scanner which resided under the keyboard below the monitor "coordinates set, ready Luna?"

"For what?" she asked with worry in her voice.

"Adventure, AVANTI!" pulling a small leaver the entire room began to shake and the cylinder in the centre began to move, on the outside several ponies had gathered at the sighting of Princess Luna with a grey stallion, even Celestia and Twilight arrived to see what the commotion was about.

"What is going on here?" Celestia spoke softly but at the same time demanding, since she wasn't happy about rumours especially about her sister, one of the guard who arrived before Celestia walked over bowing to her before reporting the situation.

"your highness, guards have reported seeing Princess Luna and a unknown Pegasus airborne and according to the public have both been seen here entering that box over there" he explained pointing in the direction of the 'box', Twilight looked over only to see the top have of what looked like the TARDIS

"but all I see is the TAR…DIS" she immediately realised that half the rumours where true as the other half was debatable as some said it was a kidnapping and other said it was Luna spending some time with that special somepony, but Twilight knew and didn't know of a way to explain it not only to her mentor but without the crowd hearing about the TARDIS, remembering The Doctors request from after the nightmare moon incident.

"_Twilight, please do not under any circumstance tell anypony I don't know about my origins and the TARDIS" _The Doctor seemed pretty serious about it and Twilight knew what time travel could do in the wrong hooves so from that day on, she swore never to reveal the TARDIS or its owner to anypony including Celestia.

"Every pony! I would like to put rumours to rest, my sister Luna is currently in her room preparing for the gala but was delayed due to her duties of guarding the night I can confirm this as I spoke with her before coming here, so please return to the gala and enjoy the rest of evening" knowing that Celestia was no liar the crowd began to disperse but as soon as they left a bright light shined in the night and the unmistakable sound of the TARDIS came to life and the Blue box disappeared but for some reason no pony noticed, only Twilight and Celestia herself saw the disappearing act of the Time machine.

"Princess, I can explain" Twilight had become even more paranoid at the clear fact of the TARDIS's existence.

"No need my dear student; I know of The Doctor and his mastery of time, it is why he called himself Time Keeper many years ago, I appointed him the royal keeper of time and the name stuck, oh I do hope Luna will have fun with him and I also hope she comes back safe" Twilight was gobsmacked but she guessed that since The Doctor could travel in time he must of met Celestia at least once in the past but that was also his future, as Twilight tried to think this through she dismissed her thought and returned to the gala with her mentor.

"Be careful Doctor"

Next Time:

Sneak Peak

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	7. Episode 7 Prologue: 30 years later

Doctor Who:

Equestrian Chronicles

**Episode 6 part 1: prologue**

**Canterlot, 30 years in the future**

Canterlot, one of the last strongholds for the Equestrian resistance, no one knew how the war started and no one knew how to end it.

Since the return of Princess Luna 30 years had passed, with the Guardians of Harmony protecting the land but now most are gone, Rainbow Dash and Rarity are reported MIA and the power of Harmony cannot be used unless all are together, pinkie broken by war (now going by General Pinkamena) is in charge of the Canterlot forces along with Commander Fluttershy (who had lost her shyness for the destruction of her home along with the death of her animal friends).

Ponyville AKA the front-lines which was lead by Princess Twilight and Lieutenant-General Apple Jack, where the main attack force against the Dark forces.

The Doctor and Princess Luna where currently in the crystal Empire along with its rulers Princess Cadence and Field Marshal/Prince Shining Armour. During the first days of the war the Empire was the first to be attacked and thanks to some Time Lord Tech the empire became the safest place on Gaia. Yet everyone that swore to protect harmony had failed to do so for 10 years, Discord was the first to fall as he along with the mane 7 (plus Doctor who is 7th) had engaged the dark forces but were defeated and Discord was imprisoned in his stone prison by the leader of the Darkness The Professor. Most citizens hoped for Celestia to defeat the darkness but the High Princess disappeared shortly before the war putting Luna in charge along with The Doctor as supreme-General of the canterlot guard but when they both addressed the public they said this war will be over in 10 years. 10 years have passed and that hope had vanished along with everything else.


	8. Episode 7: Sneak Peak

Doctor Who:

The Equestrian Chronicles

Episode 7:

**Sneak Peak**

**Canterlot Palace halls**

**VWROP, VWROP, VWROP**

As the sound of the TARDIS rung throughout the halls, the majestic blue box materialised and the door squeaked open with a young cheerful looking face popping out.

"Luna, we're here come on out" The Doctor walked out of the TARDIS now out of his suit, to avoid an angry Rarity and back with his trusty bag and tie, Luna also poked her head out to have a look around and slowly stepped out as this was her first time travelling through it. (Time I mean)

"Where are we, I'm sorry when are we" shaking her head to correct herself since she knew where she was but no idea when, The Doctor was looking at some rock which had fallen from the roof and also the shattered glass.

"About 100 years in the future, so I say the year 1100 precisely give or take a few decades" he said dropping the rocks and continuing through the halls.

"So what are we looking for" Luna asked wondering how her home got in this state.

"We're looking for a very powerful being named Harmony; the thing is I have no idea what she looks like" as The Doctor was telling Luna about their goal, the princess heard something move behind her and she turned to see several pegasi statues which looked like they were weeping lined up against the wall. "What is it?"

"Nothing, i thought I saw something move but I'll give you credit these statues definitely look old, me and Tia were talking about statues in the halls, looks like a won on that regard for pegasi" Luna looked at the statues with wonder as they looked beautiful but she didn't notice that The Doctor had frozen on the spot and his eyes wide with horror.

"Luna" he said very calmly but heavy with fear.

"Yes Doctor" hearing her Friends fear she turned to see him staring at the statue with horror on his face "oh please don't tell me your scared of some statues" giving a small laugh, but the Doctor was not in the mood to laugh.

"Look behind you" he stated not taking one eye off the statues.

"Look there is nothing to worry abo… Aaiiee" she gave a small scream to the statue which had moved clearly towards her and its face was full of bloodlust. "What in Equestria is going on!?"

"I've met their kind before, DO. NOT. BLINK!" as the two ponies stood back to back, The Doctor started to think of an escape plan. "ok here's what I've got, we could run back to the TARDIS… NO! Bad idea we would be killed before I could unlock the door, Luna can you see a door?"

"Yes" she replied shakily, scared for her life.

"Try and open it, but don't take your eyes of them, I'm guessing yours moved, so you're in more danger" Luna attempted to open the door but it was locked tight even her magic couldn't open it.

"It is locked, I could try a teleport" she inputted an escape plan but was quickly dismissed.

"No! we don't know a safe area in this time zone teleporting would ether land us in another group or attract them, so I wouldn't risk it" The Doctor continued to think and the only thing he could do was try to unlock the door himself but he then remembered it was made of wood. "god dam it, I bloody hate wood!"

"WHY! In all of Equestria would you complain about wood?" Luna shouted, not knowing the reason for her friend's hatred for wood.

"It's a long story, I'll explain later" then in a flash of light both The Doctor and Luna where surrounded by several ponies dressed in camouflage uniforms and all carrying a saddle that doubled as a weapons "WHOA!, hold it we come in peace!" it took the ponies a minute but when they saw who they were aiming at, their weapons folded away and each began to salute.

"Doctor what is going on?" Luna asked confused about the events that had transpired.

"Well it looks like they're saluting their princess" before The Doctor had a chance to answer a young voice had echoed though the room which was in fact the throne room yet it was in ruin. A couple of the soldiers moved away and in front of The Doctor and his latest companion was a young alicorn with pure white fur and a long flowing mane coloured gold and dark blue, surprisingly the exact shade of the TARDIS. As she walked towards the two time travellers The Doctor gazed at her bright blue eyes, only to be reminded of his mother.

"Who are you?" Luna asked as she too saw something familiar about this mare.

"Let me guess, Harmony" the young alicorn cocked her head not understanding why The Doctor needed to guess.

"yes, but you know who I am, I'm your…" just as the mare revealed as the Harmony that called for help a red blur shot down and knocked Harmony to the floor, after the crash a crimson red Pegasus was on top of harmony, which under normal circumstances for Luna, the entire royal guard would grab the assailant but the soldiers just shrugged it off just as they did when she used to crash into Celestia, like it was a normal occurrence.

"Harmony are you insane! You can't tell them that, they are the past versions of them!" as the red stallion who was a lot younger than Harmony shot a glance at both The Doctor and Luna. "see they look different"

"Fine! Fine!, get off Quantum" responding to the word the small pony got up and jumped of Harmony and sat next to her as she got up herself "I'm sorry, it seems you don't know us yet, I sent a message but it looks like it went to the past instead of the Crystal Empire" hearing this Luna felt a chill down her spine.

"You mean THE! Crystal Empire?" The Doctor looked at his new travel companion and wondered what this empire was as well as Luna's concern over it.

"Yes, many years ago before I was born the Empire reappeared and was retaken by the Guardians of Harmony" The Doctor knew who they where at least, he was the one who named the team of him and the girls.

"Anyway you asked for help but from what if you don't mind me asking?" both the young stallion Quantum and Harmony looked at each other wondering if it was ok to say.

"I don't think it would be a good idea to tell you, this is your future after all" as she explained her concern a male voice roughly the same as The Doctor's in age spoke up.

"Unless they already know it" walking past several of the guards a unicorn with a Dark Blue coat walked slowly and with authority towards the four along with salutes from every soldier he passed.

"What do you mean Star?" Harmony asked.

"10 years ago those two said this war would end in 10 years. Obviously it wasn't due to our superior army as we are badly losing this war, unless they already knew the outcome" the stallion explained pointing accusingly at the two time travellers causing The Doctor to walk in front of Luna to respond to hostility.

"What is he doing?" Luna thought as she saw The Doctor walk in her path in a defensive manner.

"And who are you Blue Boy?" The Doctor asked with a slight anger in his voice.

"My name is Starlight Eclipse, captain of the royal guard and the Resistance, this is Harmony heir to the throne of Equestria and the small one is Quantum Knight both are my younger sister and brother" Luna noticed something that she found odd, it was his last name it seemed familiar.

"Wait! I am the only pony in Equestria with the name Eclipse!" it was puzzling for her as she did not understand yet The Doctor however could just see the resemblance.

"Yes, I understand your confusion but I see no harm in telling you. I am your eldest son which is why I bear the name Eclipse and these two are your only daughter and youngest" as Starlight revealed the truth Luna began to feel dizzy as The Doctor eyes widened in shock.

"Wow, I didn't see that coming" he then noticed Luna began to fall to the floor "Luna!" as Luna came to after fainting from the shock, the first thing she saw was the concerned face of The Doctor "you alright" gazing into his eyes for a few minutes Luna noticed that she was caught in his arms.

"Yea I'm fine but Doctor. You can put me down now" it took a second for him to process, when he realised the position he was in with her.

"Right! Right, I'm sorry" he said adding the red colour of his blood to his grey fur as he blushed, making both Harmony and Luna to giggle. As she got back up she stared at the three you claimed to be her children, she never thought she would even settle down due to her royal duties, she never got any sleep. Yet the most important question running though her mind was who the father was?

"Well, that was a shock, at least I don't need to think of names then" Luna said trying to lift the mood as the level of awkwardness rose.

"Any way back to business, what happened here?" agreeing to discuss this matter another time the four ponies began to discuss the events that have happened in the past century.

"10 years ago, a dark castle rose from the desert followed by a tide of changelings, this army attacked every major city it could find starting with the crystal Empire, yet you had added defences to protect it from invasion and Shining armour used his protective spell on canterlot, harmony is using her magic to power the shield however it isn't perfect, we are safe from air attack but the entire city is overrun by ground forces like the statues in the hallways and ponyville is the front lines constantly under attack" as Starlight finished explaining using his magic to create a visual PowerPoint of the events, both the doctor and Luna where shocked that any attack had gone this far.

"What about the elements?" Luna asked confused at everything that her future child had explained.

"The guardians of harmony engaged the main force of the darkness without the elements but in the first ten minutes two of the group were defeated presumed dead both where Rainbow Dash and Rarity" The Doctor was now dead inside he was there and he let two of his best friends die, his anger was boiling ready to take down the source of his pain.

"Who is the main force?" The Doctor asked only to be given the name of the one person or monster that he never wished to her till he saw his own grave.

"His name is The Professor" as Harmony revealed the name The Doctors hearts stopped.

"No…that's not possible" he said quietly as he remembered one of the worst nights of his life.

**Many years ago**

"_WHY! WHY WOULD YOU DO THIS! This isn't us, this isn't you WHAT ABOUT THE PROMISE, DOESN'T IT MEAN NOTHING TO YOU!, DOCTOR! ANSWER ME GOD DAM IT!" The Doctor (human form) cried over a young girl who was bleeding heavily and was clearly dead, in front of him was another, another Doctor holding a blood stained knife and a look on his face that showed the pain The Doctor had suffered over and over again and he had enough and it was time for blood._

"_hmm, I haven't forgotten it, but yet I don't give a dam about it, YOU WANT TO CONTINUE TO UPHOLD THE LAWS OF THOSE BASTARDS I CALL MY KIND FINE! BUT WHAT I DID IS A SMALL TASTE OF WHAT THEY TOOK FROM ME!" both Doctors kept eye contact one mourning the loss of his friend the other happy to cause the pain "never call me The Doctor again, I like Professor much better"_

**Present**

The Doctors eyes where now cold with sorrow and anger, causing Luna to be concerned.

"Doctor? Are you ok?" as he lifted his head Starlight took a step back, he knew to fear the Doctor when he was in this level of anger yet never witnessing it firsthand.

"you tell me exactly where this castle is so I can pay myself a visit" The Doctor walked towards the wall as his cold eyes lay on the sword hung on the wall, ready to for the first time in 100 years…TO KILL.

TO BE CONTINUED

Next Time:

Fear The Pink Mist

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	9. Episode 8: Fear The Pink Mist

Courier:

Doctor Who:

The Equestrian Chronicles

Episode 8:

Fear the Pink Mist

**Previously on Doctor Who: Equestrian Chronicles**

"Where are we, I'm sorry when are we" Luna asked shaking her head to correct herself since she knew where she was but no idea when.

"About 100 years in the future, so I say the year 1100 precisely give or take a few decades" he said answering her question.

"So what are we looking for" Luna asked wondering how her home got in this state.

"We're looking for a very powerful being named Harmony; the thing is I have no idea what she looks like"

"The guardians of harmony engaged the main force of the darkness without the elements but in the first ten minutes two of the group where defeated presumed dead both where Rainbow Dash and Rarity" The Doctor was now dead inside he was there and he let two of his best friends die, his anger was boiling ready to take down the source of his pain.

"Who is the main force?" The Doctor asked only to be given the name of the one person or monster that he never wished to her till he saw his own grave.

"His name is The Professor" as Harmony revealed the name The Doctors hearts stopped.

"No…that's not possible" he said quietly as he remembered one of the worst nights of his life.

The doctors eyes where now cold with sorrow and anger, causing Luna to be concerned.

"Doctor? Are you ok?" as he lifted his head Starlight took a step back, he knew to fear the Doctor when he was in this level of anger yet never witnessing it firsthand.

"you tell me exactly where this castle is so I can pay myself a visit" The Doctor walked towards the wall as his cold eyes lay on the sword hung on the wall, ready to for the first time in 100 years…TO KILL.

**Continuation**

"Are you seriously thinking going there? No offence but the last time you where there you almost died and that was the future you!" Starlight was now trying to convince The Doctor to stop and think as he was on a blood fuelled rage that Luna, Harmony and Quantum could not understand.

"WELL YOU SAID IT YOURSELF, HOW COULD I KNOW IF THE WAR WOULD END IN 10 YEARS UNLESS I KNEW THE OUT COME, MAYBE I LOST THEN BECAUSE IT WAS A FIXED POINT, WHAT EVER THE CASE IS, I DON'T GIVE A DAM, THAT MONSTER IS GOING TO DIE AND IM GOING TO BE THE ONE TO CHOP OF HIS DAM HEAD!" his eyes know red with rage he had flown up and removed a sword from its stand hung on the wall "Luna, is ok if I borrow this" he asked now lowering his voice trying his best to calm down.

"Yes you may, but I must protest you said yourself one time that there is no need to harm if there is another way, is killing this person really going to return everything to the way it was, wouldn't be better to imprison him and make him stand trial for his crimes" Luna was clueless as to how The Doctor knew this Professor and why he had such a drive to kill him.

"I'm afraid that would do much" Starlight had strapped on his combat saddle and sheathed his own sword ready for combat.

"What do you mean by that?" Luna asked her Eldest as he prepared for battle.

"This is not the first time The Professor has appeared in fact his last appearance, he was stopped and sentence to death by age and for a Time Lord that is a long time" as Harmony explained that The Professor was already guilty of crimes that earned him a Death sentence, the first in her memory, she had recognized the Name Time Lord.

"Time Lord? But Doctor isn't that you're…" The Doctor turned around still with cold eyes and looked at the night blue mare.

"yes he is, but it goes a lot deeper than that, he is what I never became" The doctor took a piece of paper out of his tie and opened it up to reveal a photo, he placed it on the table which was set up in the middle of the throne room and What Luna saw made little sense, it was a picture of two People that where obviously not ponies, A young man wearing a black leather jacket and a Tartan tie which along with the style and colour of his hair matched The Doctor making Luna guess that is what he looked like before he arrived in Equestria, next to him was a young girl with long blonde hair and wearing a light blue sweater both had a large smile on their face as they had taken a photo in front of what looked like the Eiffel Tower in Prance "the Professor is from another universe but he jumped to mind to escape his own fate which was decided by the Time Lords, once he met me he found out that the Time Lords where gone, Destroyed in the Time war and so he decided he should exact revenge on the universe, that my people worked hard to protect for 100 billion years. I stopped him but at a price, that girl in the picture was the last friend I brought onboard the TARDIS and he killed her in cold blood and since that day I vowed on my own grave that I would be the last thing he would ever see" The Doctor took back the picture and returned it to the slot in his tie "after the Nightmare Moon incident, I saw that my coming here would allow me to make a new life and live peacefully but no, HE HAD FOLLOWED ME! HE WILL PAY FOR THE LIVES HE HAS TAKEN AND STEPPED ON, WITH HIS BLOOD!" The Doctors bloodlust reaching the point of insanity Luna had heard the story and was prepared to fight this battle along with her best friend.

"Then I will fight alongside you, this is my kingdom and no matter when I am from it is my duty to protect Equestria from hostile forces" Luna said placing a hoof on The Doctors shoulder as he stared out into the fallout of the 10 year long war.

"I will make my way to the Crystal Empire to inform both your future selves, so they can prepare to fight back following your lead" before he prepared to leave he looked back to Luna who spotted him glancing at her.

"Is something wrong Starlight" Luna said slightly worried.

"Nothing Mother, it's just its been so long since you had your hair like that I forgot how it looked" as tears began to fill her eyes Luna walked over to the throne and pressed a small button and following a secret compartment rose from the floor revealing two spaces for armour yet one was missing, the one remaining was a black armour which was covered in battle scars and looked like it fought in an incredible battle.

"Is that yours?" The Doctor asked as he examined the battle damaged set of armour.

"indeed, it was the very set of armour that I wore during the fall of the Crystal Empire over 1000 years ago…" as Luna moved towards her old armour the other space which was disturbingly empty rose some questions in Luna's head "Starlight I wish to know, where is my sister?"

**Castle of Darkness**

In the middle of the desert a black castle stood surrounded by changelings and covered in angles, inside the throne room of this grand castle sat an olive coloured unicorn reading a book, a Pegasus with bat like wings appeared and bowed before the unicorn.

"My lord, you called for the prisoner" after catching the unicorns attention he placed a bookmark in his book and put it down while several changelings dragged a white wounded pony in front of the unicorn. Unlike most ponies he sat relatively like a human and as he got up from his throne he walked down on his hind legs alone and when he was within reaching distance of the prisoner he swiped the bag from over her head to reveal.

"High Princess Celestia so good of you to visit, how long has it been since your last beating" with the bag removed the wounds that the princess suffered looked far worse than they did earlier, it was also apparent that her mane had been cut very short and the majestic rainbow colour it had had faded into a blood stained pink.

"Professor, when will you end this madness?" the unicorn revealed as the Professor gave a small chuckle as Celestia struggled to lift her head.

"You know that reminds me of a film from a small backwater planet I know of, but really I will stop as soon as The Doctor is dead or better yet bowing at my feet. But no, he continues to resist and prevent me from taking the Empire but what shocks me the most is that he hasn't attempted a rescue" he replied whole walking around the battered monarch before sitting back on his throne.

"He does not need to, he knows that you will fail just as every other has before you" this was followed by a maniacal laugh along with a hard kick in the face from The Professor.

"Hahaha, but did any of the others last TEN WHOLE YEARS! Yes there was Discord but look at him now, reduced to a hat rack" pointing at the statue of discord in a protective stance as well as being covered in hats "the guardians of harmony are powerless, canterlot is in ruin and you can't do anything to stop me" despite knowing it would only lead to pain when The Professor came close to Celestia's face she spat right in his eye, followed by a quick slap "bloody bitch!, TAKE HER BACK TO HER CELL! And give her an hour long torture session to liven her up a bit" the Pegasus that brought in the prison bowed once again to his master.

"Yes my lord, TAKE HER AWAY!" replacing the bag onto of her head, the changelings tugged at the chains imprisoning Celestia and began dragging her back to the dark cell she has known as hell for the past ten years.

**Canterlot palace**

"So not only is this a take back, it's also a rescue mission" The Doctor had put on a set of armour that Harmony had given him and Luna was also suited up ready for war.

"Yes, but we have had no intelligence or evidence to confirm that she is there" Starlight was going to alert the future versions of The Doctor and Luna but thought it best to brief them on the area they had to fight though.

"She'll be there, knowing him he likes to cause pain on others especially prisoners, my only concern is if she could survive 10 years of tortured, unless she knew something he wanted to know, then he would beat her till near death then prevent it so she could be interrogate again" the thought of her sister in pain for so long was disturbing but she knew she would not give up so easily.

"I hope your right, anyway to get to the desert you will need to go around ponyville…" The Doctor held up a wing to object Starlight's idea.

"Wait if we are going to have a chance at beating The Professor we will need the elements" this made Starlight a bit uneasy as he did not want to tell him.

"That's not going to be possible" he said with regret in his voice.

"Why not, you're the one who said that Rainbow and Rarity where MIA so if we pack the elements we can put a end to this quickly" he said still with a slight anger in his voice.

"The only issue is that the elements have been missing for decades and they won't work, both General Pinkamena and Commander Fluttershy have changed due to the war, you may get Fluttershy as she only seems to have lost her shyness but I'm afraid even Pinkamena is beyond even our help, she hasn't laughed since…" expecting The Doctor to complain he held up his wing as to say he understood, this was not the same Doctor This was a warrior.

"That's is not important, ether way we need at least the guardians if we are to have even a fighting chance" seeing The Doctors point he placed a map on the table and rolled it out.

"In that case we can send the General a message to gather for an emergency meeting on the train to ponyville, normally she would refuse but if you both sign the notice she won't have a choice the Commander will most likely attend with her. Then you just explain the situation and she should join you" it was a lot to take in as Luna was struggling to keep up, normally she was the one giving orders.

"_Now I know how the men felt during the fight against Sombra" _Luna thought to herself as she listened in.

"Then once you get to ponyville you will find Twilight in her palace…" then the bright side of The Doctor emerged yet only for a second.

"Whoa, whoa, whoa, hold it, I know see likes that tree of hers but it's no palace" unsure of what to tell both of them Starlight decided to avoid that topic.

"uhh, spoilers?" he said with a cheesy grin followed by The Doctor eyebrow lifting to show he was not amused "anyway, once you meet up with Twilight it will be just a simple charge to the castle, once I alert both of you at the Empire, I will try to send reinforcements" with a small nod from The Doctor, Starlight's horn lit up and he began a teleportation spell "good luck" Starlight wishing The Doctor and his mother luck before he zapped himself to his new location.

"What now?" Luna asked sheathing her sword after polishing it during the briefing, with The Doctor giving her a look she recognized from her father

"Now we move" following The Doctors words she began a teleportation spell of her own, inbound to the train station.

**Canterlot Station**

Since original equestrian weapons were ineffective against hoards of changelings The Doctor had reluctantly given the Canterlot army weapons similar in function to the very weapons he loathed, ballistic in nature it had turned most of Equestria into what he called Afghanistan. After receiving a notice signed by Princess Luna and The Doctor themselves, The main defence squad lead my General Pinkamena headed for the station only to be engaged by enemy forces moments after leaving the defence shield.

"What now, we are outnumbered and the General has pulled a Hoofdini on us" two soldiers had taken cover from the onslaught of the enemy behind the clock in the courtyard of the Train station after being ordered to scout the area, the one complaining was taking pot shots at the enemy to prevent the enemy advance and the other was bleeding from a magic blast to the leg.

"Stop your belly aching, remember The General always has a plan" upon those words the entire enemy line exploded followed by a lone figure that had jumped over the two soldiers and stood in front holding a massive cannon leaning on her shoulder in one hand and a SMG in the other, as several of the changelings recovered from the explosion along with others arriving, the figure standing on it hind legs lifted her head to reveal her pink fur under her black trench coat and equally pink straight hair along with the only part of her body which was not pink her piercing blue eyes "see what I mean" the soldier said before taking cover from the massacre about to take place.

"Let's party" seconds later both The Doctor and Luna had arrived outside the train station to see the entire courtyard covered in blood and standing in the middle was a pink mare wearing a blood stained trench coat.

"Pinkie is that you?" The Doctor before the figure turned and threw a knife for The Doctor only just able to dodge it "Dam it Pinkie, you could of killed me" looking back to see the knife destroy a wall under the sheer force of the throw once he turned round he saw a 9mm pistol outfitted to her hoof so she could it correctly, aimed at his face.

"and I told you to stop calling be Pinkie" The Doctor was scared out of his mind he had no idea that Pinkie could be this dangerous but as the pink mare looked at his fore head she sheathed her weapon "Sorry Doc, didn't realise you where from the past but still don't call me Pinkie" the doctor gulped after coming inch away from death by one of his best friends, Luna was just confused about the whole situation.

"Pinkie, uhh I mean Pinkamena what happened here?" Luna asked as Pinkamena as she walked over to the two soldiers who were resting by the clock.

"We got a royal notice ordering both me and Fluttershy to met here, I guess that was from you" as she finished several pegasi and a chariot retrofitted for medical purposes arrived along with several soldiers and Fluttershy.

"Doctor! Ohh it is so good to see you!" Fluttershy had crashed into the Doctor giving him a hug, which was very unusual for her as pinkie signed some paper work to discharge the soldier for a medical leave.

"Fluttershy, you have changed usually you would barley say hello" Fluttershy was then pulled back by Pinkamena allowing The Doctor to get up.

"Commander this is The Doctor from the past, probably just after the Gala" both Luna and The Doctor where shocked they never knew Pinkie would even guess that.

"Ohh, well ether way I haven't seen you in a long time, it's nice to see you both again" there was a definite change in Fluttershy normally she wouldn't do half the things she just did unless she was furious.

"So what did you want us for and why didn't your present selves come instead?" pinkie had sat down on a rock waiting for the two to explain themselves.

"We are going to raid The Professors palace and end this war" according the Starlight, pinkie would of agreed in a heartbeat but instead proved him wrong.

"No" this shocked The Doctor and Luna as she was needed to end this 10 year old hell.

"What!" Luna exclaimed as she was about to lose her temper.

"Don't lose your temper over me princess, if you're from the past then you know the future so why didn't you end this before it could begin" Luna was going to knock some sense into the pink pony but decided against it hoping she would change her mind.

"I couldn't, that day, that first loss was a fixed point, I know future events if I change those then my reason for doing so disappears causing a paradox which I cannot allow, it would destroy everything" she never seemed it but Pinkie was very smart and she could understand where the Time Lord was coming from.

"Fine I will help but it's because I owe you quite a bit, if it where up to me I would rather die fighting" with both Pinkamena and Fluttershy both agreeing to help all four entered the train and it began to move towards Ponyville.

TO BE CONTINUED

Next Time:

Return Of Darkness

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	10. Episode 9: Return of Darkness

Courier: ok before you read this I must correct several things, first every episode set in the future will be known as the war arc as this is going into a classic style doctor who cluster, two this will be set 30 years in the future instead of 100 as the mane 6 would still be around and I don't plan to have any episodes 100 years in the future but you'll have to wait for that and finally the element of trust is going to get a cosmetic and power change so read the one shot "origin of the elements" when its released

Well enjoy

Doctor Who:

The Equestrian Chronicles

Episode 9:

Return Of Darkness

_**Train inbound to Ponyville**_

Hours away from the frontlines The Doctor, Pinkamena and Fluttershy had begun discussing their plan for attack while Luna scouted ahead

"So Doc, what's the plan?" Pinkamena asked while pouring a drink from the carriage bar

"It's Doctor and we need to find Twi and AJ, then we launch a final assault and take the castle…can you pour me one of those as well" it seemed that since the palace The Doctor has calmed down and was back to his usual goofy self Pinkamena rolling her eyes as proof

"Not possible, the last time we tried to assault The Professor we lost a third of our troops" Fluttershy said with confidence making The Doctor feel uneasy "what?" Fluttershy asked noticing The Doctors discomfort

"Sorry it's just weird you talking like everypony, took me weeks to get a sentence out of you when we met" he explained followed by Pinkamena passing a glass of alcohol "ooh scotch whiskey, this trains got class"

"I didn't know you drink Doctor" Luna said surprising The Doctor from behind

"Ahh! Luna! Don't do that and I don't drink very often but I'm more relaxed after a drink, used to have several each day during the Time War" he said before downing his glass making everyone's eyes widen as his glass was full "what?"

**Ponyville Station**

Receiving word that high ranking officers would be heading for the front lines, lieutenant-general Apple Jack sent a squad to greet and escort them to the Ponyville palace.

"So sergeant, who's coming? Do you know?" one soldier asked his commanding officer while both stood waiting for the train in front of the squadron escorts

"Nope but most likely it's going to be General Pinkamena since the train is coming from canterlot" the sergeant said looking at the clock on the ponyville tower two blocks away

"Hold on I hear something sarge" the soldier notified the sergeant and upon looking up the tracks a light could be seen piercing the dark veil of the night (the nights have become longer to provide better cover for troops)

"Good, right on time. At attention boys the guests have arrived!" following their commander's orders the small squadron all lined up in formation ready for the VIP to show. With the train slowing to a stop the door slid open and to the sergeants surprise stood Princess Luna

"Your highness!?, I was expecting General Pinkamena" Luna was slightly puzzled then she remembered that her future counterpart spent most of her time at the crystal Empire and wasn't seen often on the front lines

"don't worry she's here too" The Doctor said moving in front of Luna which shocked the sergeant more than Luna's presence

"Supreme-General Time Keeper!?" unsure what to do the sergeant did the first thing he thought of "Canterlot guard! General on sight ATTENTION!" then every soldier in the station in eye view of The Doctor saluted him, not Luna, him

"Uhh, why am I getting the royal treatment? Shouldn't she be getting that? I thought I was a military advisor" the sergeant lowering his hoof looked at The Doctor with confusion

"I don't understand Sir…hey where is your" and before he could finish his question the sergeant caught sight of General Pinkamena Shaking her head signalling him to stop

"Where's my what? My hat?" he asked then looking to Pinkamena "do I wear a hat in the future? It's a fez isn't it?" again rolling her eyes, Pinkamena stepped out of the train and addressed the squad

"listen up colts and mares, we are here under executive orders and those are not to be questioned, both Princess Luna and S-General Time Keeper that you see before you are previous versions of the ones currently in the crystal empire, so you are forbidden to mention anything from the past 100 years to them without my express approval, is that understood" with Pinkamena issuing a gag-order on the squad, the entire group in question braced up in response

"YES GENERAL!" upon finishing her quick briefing on the situation the squad of soldiers began to lead the every growing guardians plus Luna to The Doctors best friend Twilight Sparkle

"you didn't answer my question 'General'" Pinkamena gave a cold look to the Time lord that he swore had the same effect his step-mother River had on him. Despite being on the frontlines, Ponyville itself was pretty secure as there were no fire-fights in the town centre "hey, isn't Twi's place that way?" The Doctor had noticed that they were heading for the outskirts of town instead of the centre where Luna and The Doctor knew Twilights library was

"long story, just wait a few years" Pinkamena said coldly as she walked past him with both Luna and The Doctor Looking and shrugging at each other.

**Friendship Castle**

"Here we are sir, I just need to radio General Apple Jack" the sergeant explained going for his radio but was halted by a familiar Texan voice

"no need soldier, I see em" standing in front of the group was Apple jack suited in combat gear like everyone else with the only difference being her trademark hat yet with a large hole in the side

"AJ!, man is good to see you" The Doctor ran up to greet his friend with a hoof shake that they both made after a night out, days after arriving in this universe and judging by apples response to it, they've used it for a thirty years

"Likewise Doc you too your highness and I now about that timey wimey thing you got going on so let's get this over with" relieving the squad of duty Apple Jack led the in to the castle supposedly owned by Twilight

"My oh my, Twilight lives here, it beautiful" Luna exclaimed stunned by the natural beauty that her home never really had outside the royal gardens

"that'll be right Princess, it's a long story but you'll find out eventually" it seemed that out of the 3 of the mane 6 the doctor has met in this time only Pinkie seemed different, Fluttershy had also changed but for the better she had more confidence without changing her personality but Pinkie had become the one thing she hated a party-pooper, Apple Jack on the other hand seemed right at home she was always strong willed and her attitude proved that "now Doc, Princess allow me to introduce Princess Twilight Busy-pants" in what appeared to be the throne room, since there were 7 thrones all in a circle each with the cutie mark of each of the guardians even The Doctor but looking ahead he saw his dear friend twilight sitting in her throne which was moved to the centre against a large map of Equestria which showed everything in real-time, the purple mare on the other hand was talking to one of her Guards and looking more busy than The Doctor had ever seen her, but he was more interested in the map

"Wow, cool map" The Doctors youthful glee caught the attention of Twilight who looked over to see the physician 30 years younger (despite the fact he never ages)

"Doctor!" shooing the Guard away Twilight then stepped off her throne and walked towards the Time Lord and gave him a hug

"Hey Twi, long time for you I bet" The Doctor greeted his first equestrian friend making Luna raise her eyebrow unknowing to most including herself in what appeared to be

"Somepony's jealous" Apple jack whispered to Luna causing her to blush and scream form the top of her lungs

"I AM NOT!" everyone jumped in surprise of the use of Luna's trademark equestrian voice causing her to blush even more and walkout the door followed by directions from Apple Jack

"Bathroom's on your left!" Apple Jack yelled to the embarrassed Princess as she later burst out giggling, even getting a smirk out of Pinkamena.

"Right, that was random" The Doctor said confused out of his hyper intelligent mind "anyway Twilight I probably already said this but congrats on the coronation but I'm afraid we need to get down to business"

"yes very well, as you can see the most direct route to The Professors castle is currently the frontlines, so if you are heading there like Starlight had said then you will need to go around" twilight explained to the group pointing at the real-time map

"No we need to go straight down the middle" The Doctor said after a pause

"Wait what!? Are you crazy you can't go direct is suicide" Apple jack shouted just now hearing his words

"Well we're not going around, I know the Professor more than anyone and going around is too risky, we would no doubt be killed or worse" The Doctor said now in his trademark thinking pose

"So what do you suggest then Doc?" Pinkamena said from behind the Time Lord when an idea had struck him

"We need to gather the guardians and rescue the princess so what better way than to do it then to guaranty our safe passage" he said turning back to face his group of friends "we need to surrender"

"That's a terrible idea! We'll have no way to fight back once we're inside" Apple Jack noted as they would be striped of weapons on the spot

"That's easily fixed, watch" and with that he took a key on a string from his bag and slung it round his neck, causing his armour and weapon to vanish

"Oh my, where did your weapon go?" Fluttershy stated as she could not see anything he was wearing

"low-level yet powerful perception, The Professor and his army wont bat an eye as they won't notice your weapons" with that he took several more keys out and gave them to each of his friends "right ladies gear up, the perception filter will make your weapons unnoticeable but as soon as your draw them the filter loses affect" as each pony took a key they left to prepared and each came back with their own weapons, Fluttershy had her extendable spear, Apple Jack had a Katana, Luna (returning from the bathroom) kept what she had on and Twilight had walked away and picked up another sword from behind The Doctors future throne

"Doctor you're going to need this" Twilight said with her soft yet serious tone presenting the finely forged blade to The Doctor, him taking it yet not knowing why

"Why, I already have a sword" The Doctor was sure this was key to his future as the blade gave off a vibe that he though felt familiar

"you told me ten years ago to give this back to you when the time was right, I think now is the time, Time Lord" The Doctor stared at the sword, it was light, very light, lighter than the sword he carried presently and he felt a connection between himself and this blade, like the bond he had with his TARDIS, so he replace the blade with the new sword and was ready for battle

"Right team, let's go kick some flank" The Doctor said before the newly rebuilt guardians of harmony left to commence there terrible yet brilliant plan

**1 hour later, Castle of Darkness**

The professor was busy once again in his book as one of his minions entered the Thorne room causing The Professor to shut his book in annoyance

"What! You know I ordered no one to disturb me between 1 and 4 o'clock" he shouted looking down at his subordinate

"My apologies my lord but we have the remaining guardians including Princess Luna" this made the Professor throw his book towards the wall something he has never done before

"The Doctor as well" he said getting up on his hind legs

"Yes my lord" the minion said raising his head

"well what are you waiting for! Send them in, send them in" The Professor shouted before running back up to his throne downing a twirl before sitting down and with a signal from the minion The Collection of The Doctor, Luna, Twilight, Apple Jack, Fluttershy and Pinkamena were lead in but several guard "oh! My dear Doctor, so good of you to visit"

"Professor, though bit of advice, Olive not your colour" The Doctor said ignoring the many spears pointed at him as he walked toward the throne

"ahh still as witty as the day we met, though I see you don't have a…" was the professor looked at his nemesis he noticed that The Doctor he was looking at wasn't the one currently hiding in the Crystal Empire "Oh! Doctor you slick devil, no wonder you saw my invasion coming you've known about it for decades, let me guess psychic message gone wrong"

"as usual your deduction is spot on, is that Sherlock Holmes and the masked bandit, written in England august 3rd 2183" it seemed that both Time Lords were equal in intelligence but obviously The Professor had the upper hand

"very well done but this meeting will be short lived as I can't kill you since it would erase the time line but I'm sure you will enjoy your stay here, take them away" as The Professor turned away The Doctor began to draw his sword with his wing and in a split-second The Doctor had shot towards his foe and his blade connected with a golden spear held in mid-air by a red magical aura also presently covering The Professors horn who was now on all fours to increase his balance "WHAT! You think I wouldn't see though you perception trick but truth is I'm been longing for some BLOOD!" The Doctor struggled against the strength of The Professors magic but still held his own. The battle had begun

"NOW!" following The Doctors command the entire group engaged the castle guards each taking several at a time, both Apple Jack and Fluttershy stood back to back fending off their share of guards

"Don't worry sugercube I got your back" Apple ensured her friend drawing her blade with her mouth at first slowly but then quickly causing most of the guards swords and spears to be chopped in half

"Likewise" Fluttershy replied clashing with several guard with her one spear, Twilight was using her magic to repel and incapacitate her foes, Pinkamena had began taking on the bulk of the force that had entered the throne room using all manner of weapons and Luna was fending off her own share using her own Lunar magic and sword all while The Doctor and The Professor went all out on each other

"Hahaha! Just like old times huh Doctor" The Professor said while taking quick jabs at his adversary giving The Doctor a few cuts but unable to wound him

"SHUT IT!" both Pegasus and unicorn where equal in skill but yet The Doctors hatred and speed seemed to give him the upper hand but to The Professor this was not the first time they had fought and as The Doctor went for an opening The Professor had made he was surprised to see a second blade, The Professors spear had spit in two and he had cut the doctors left wing causing him to lose his balance and fall down the large set of stairs falling unconscious

"this is it Doctor prepare to die!" now only wanting the pleasure of killing his foe ignoring the consequences he reconnected his spear and leaped down the throne stairs and aimed straight for The Doctors head but instead of piercing his flesh The Professor was deflected by another sword held by the magic of Luna, who was now enraged

"You shall not harm him" she said coldly giving The Professor a cold shiver down his spine, he had yet to face the Princess of the Night

"what are you going to do about it princess" and following his taunt Luna sped towards The Professor only just able to block her attack and was unable to strike her, Since he was unable to hold off an Alicorn The Professor resorted to his own magic that he developed inspired by one of his favourite stories, spinning the spear he spoke the word of his spell before slamming down his weapon on the ground on the ground causing a ripple of red energy

"_GRAVATOUS!" once the ripple had passed over Luna her magic was nullified and she fell to the ground causing the ground to crack below her along with everyone else that was affected by the spell. Now above Luna pointing his spear to her heart ready to wipe her from life itself The Doctor had awoken to see Luna only moments from death_

_"You know what I'm disappointed, your sister was way better, well night night" Luna's eyes widened in her despair as she was unable to protect the one pony who actually cared for her beyond her sister, she looked over to The Doctor who was struggling to get up due to the gravity magic and was happy to have known such a caring pony to which she had looked back at all the moments she had known him and finally she knew what she felt that moment she saw him only a day ago at the gala, she said looking at The Doctor yet not loud enough for him to her_

_"I love you" and at that moment the Professor struck_

_"LUUUNNNNAAA!" The Doctor screamed finally regretting bringing her to this hell of a future but to his shock the Spear had not hit her_

_"What the?" The Professor exclaimed attempting to redo his attack but was unable to move his weapon like someone else was holding it _

_"my apologies but I cannot allow you to harm this body" the voice came from Luna but was clearly not her and to everyone in the room but The Professor they knew that this was not a good sign even more so when purple mist surrounded the Princess and the dark Time lord forcing him to teleport several feet away, then as Luna's body stood up her mane becoming the colour of the mist her eyes shot open and her iris folded into a cat like slit along with her entire eye colour turning turquoise looking majestic yet demonic at the same time_

_"You're not Luna, who are you?" The Professor had no idea what he had unleashed and The Doctor tried but failed to get up to snap Luna out of it but it was far too late_

_"I am a Nightmare" and upon those words her entire body colour faded from night blue to pitch black Nightmare moon had returned_

TO BE CONTINUED

Next Time:

Rise Of The Keeper

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	11. Episode 10: Rise of The keeper

Doctor Who:

The Equestrian Chronicles

Episode 10:

Rise Of The Keeper

Everyone in the room was staring at Nightmare Moon as she herself was looking around noticing The Doctor on the ground.

"Doctor, such a long time it's been. How are you?" she said walking over to the Time Lord unaffected by The Professors magic and lifting his chin to get a good look at his face.

"Nightmare, i thought you where destroyed" Nightmare gave a small chuckle before turning away from The Doctor and looking at all the others who foiled her plans for eternal night.

"Of course not, you destroyed the parasite, I myself am eternal" the idea hit him like pinkies party cannon, it made complete sense, he figured Nightmare Moon was a separate conscious but never suspected it to be a parasite.

"But if I destroyed a parasite then, what are you?" she was about to answer the question but The Professor wasn't one to like being ignored.

"Excuse me but weren't we doing something here" Nightmare snapped her head towards The Professor causing him to take a step back.

"How rude, normally I would kill you and be done with it but you have earned the right to die slowly" she said using her magic to lift Luna's sword which at a swing turned into a scythe and The Professor lifted his spear and both were about to go at it.

"Bring it" The Professors cockiness was misplaced because as soon as he finished, Nightmare had her weapon to his throat yet he teleported before losing his head but he had a deep cut on his neck to show for his arrogance yet it healed into a scar only seconds later "I take it back, you are good"

"You fool! never compare me to my weakling other half, she has the potential and the skill as we are one in the same but I am much more willing to do what is necessary to survive!" and she shot off with incredible speed only for a loud bang to ring through the throne room and Nightmare Moon landed on the ground next to The Doctor with her shot in the chest.

"What? Who took that shot?" The Doctor said looking around following the trajectory but the culprits identity shocked him and everyone else who saw her, The Professor however just laughed his face off "what…no, no! PROFESSOR WHAT HAVE YOU DONE!" now beginning to push the gravity magic still in affect enough to stand up yet barley in order to attack he was pushed back down and then he had a high caliber sniper rifle pointed at his face.

"Hahaha, who would off thought that this stylish dress maker would be such a good shot, thank you Rarity my dear" The Professor said gloatingly while sniffing a portion off Rarity's well kept main and to everyone's shock except for Nightmare since she was unconscious from blood loss, Rarity seemed to enjoy him playing with her hair.

"That there can't be Rarity she would never let anyone touch her hair especially a monster like you!" Apple Jack shouted making Rarity giggle in a sinister way.

"Oh, I assure you Apple Jack, I am the real Rarity and this monster has promised me the stars" she explained waving her hair out of her face still aiming the rifle at The Doctor.

"Hefty promise considering you don't have a TARDIS and that Vortex manipulator you stole only carries one without overloading" The Doctor explained gaining a swift kick in the face by Rarity "ow!, ok tell me was that for talking or something I did in the past" Rarity wasn't playing games and instead of hitting him again she cocked her weapon and took aim "shutting up"

"Don't worry Doctor we have plenty of time to interrogate you all for the location of the TARDIS" The Professor said finally before pointing at a guard who was released from the gravity spell "you there take them to the holding cells and give them a first aid kit, I want that one alive" he ordered referring to Nightmare Moon.

**Castle of Darkness holding cells**

As everyone was dragged and flung in the holding cells along with a medical kit so The Doctor could tend to Nightmare, Pinkamena on the other hand went ballistic.

"OK! What the F***, why is Rarity on his side!" Pinkamena yelled after her cell was locked.

"Well I know powerful brainwashing techniques and how to reverse them if needed, most likely he does too, the fact she is such a good shot is unbelievable, I got to explore that when we get…if we get back" The Doctor explained firstly with anger then glee followed by sorrow, everything went from bad to hellish, he wasn't even sure if Nightmare Moon returning was a good thing or just a disaster waiting to happen.

"Sister?" a weak voice spoke from the cell next to The Doctors and inside was a heavily wounded Princess Celestia.

"Celestia!?" everyone said in surprise.

"You're still alive" The Doctor followed in relief.

"Indeed but I am very weak, I doubt I will live to see my kingdom again. My sister will finally have the crown to herself, I'm just glad she won't rule alone" Celestia voice was incredibly weak and her body was fragile as glass, this wasn't surprising, The professor must off starved her in order to get information However The Doctor could not stop looking at Celestia mane, it had been cut near his hair length not to mention the lack of other colours as her hair was bright pink with bits of red that looked like blood.

"Don't say that your highness, I'm going to get us all out of here and by the end of the week you can all have a party" the Doctor stood assuring his friends and any prisoners among them.

"Not hosting" Pinkamena said coldly while stitching her trench coat.

"You've become what you hate" The Doctor said to Pinkamena as Nightmare stirred and began to wake up.

"Uhh, where am i?" Nightmare asked unable to get up due to pain.

"You are in The Professors Dungeon dear sister" Celestia said regaining some of her strength but still very weak.

"Celestia that is not you sister" another voice spoke from across the room in another cell, it was difficult to see due to lack of light but The Doctor could confirm from the voice and being used to seeing in the dark.

"Rainbow, glad you're still alive" as The Doctor confirmed the voice as Rainbow Dash, Twilight, Fluttershy and Apple Jack all rushing as close as they could to greet her.

"What do you mean Rainbow Dash?" Celestia asked unable to see the physical changes to her sister again from lack of light.

"She saved my life and fought The Professor and she would have won but that psychopath had developed his own kind of magic causing Luna to lose her greatest strength, her speed and as a result to prevent her death the consciousness that had developed from the darkness which possessed her before I arrived surfaced, in short what you can see is not Luna but Nightmare Moon, I'm Sorry" despite being told the very being that forced her to banish her only sister was still alive let alone not knowing that both this Nightmare and The Doctor came from the past, she wasn't concerned, almost like she already knew in a way.

"It would not matter ether way Doctor, Nightmare Moon or not she is still my sister" Celestia spoke with her usual confidence and reassurance but despite that no one could look at Nightmare knowing what she had done.

"Oh well glad to know 'sister' but I really don't give a dam, hey you Time boy, what happened?" Nightmare asked after replying to Celestia with rudeness and sarcasm.

"you were shot before you could give the final blow and before you ask it was Rarity" hearing of her defeat prompted her to get up to gather her bearings but was halted by the caring nature of The Doctor "whoa, whoa hold Miss Midnight Terror I care nothing about you but Luna body needs to rest, so DO. NOT. MOVE" with a momentary staring contest between Mare of Darkness and Lord of Time, The Doctor began to help Nightmare Moon up and propped her against the cell wall.

"Thank you, it was getting cold on the floor" Nightmare said in her own genuine gratitude.

"So you guys got an escape plan? Because this hotel has had some bad room service" Rainbow asked with her usual coolness while pouring the gunk in her bowl on the floor.

"First we need to know everything we can, ok Rainbow can you tell me exactly what happened to Rarity" The Doctor said while looking through a small bag he took out from his tie collar

"Well, if Rarity IS brainwashed then it must have happened after she sold us out" this information surprised the group excluding the royal sisters as one already knew and the other didn't give a F***

"What! How?" Twilight said distraught to hear that one of her closest friend could have potentially betrayed her.

"well remember that nice big shield over ponyville, guess how rotten olive knew how to bring it down quicker that he should have and that's not the first, that selfish bitch has been giving him key information in exchange for luxuries" this brought everyone's hearts down, war really could change a person's loyalties but The Doctor was not convinced.

"HOLD ON! Ohhhh that is brilliant! But it makes perfect sense!" everyone perked up wondering what The Doctor was giddy about this time.

"Doctor what is it?" Twilight asked on behalf of the entire group.

"Ok Rainbow, am I correct to say I made the shield for ponyville correct?" The Doctor trying to connect all the pieces he had collected.

"Yea, we were all there when you set up the shield for canterlot, ponyville and the Crystal Empire what's that got to do with anything?"

"Sooo, if we all were present when I made the shield generators then you all should know how to disable them from inside and out but I noticed that ponyville had Ion-pulse Cannons and Anti-Air Turrets preventing complete invasion but the need for constant care at the frontlines and also in Canterlot, Harmony was there creating a protective barrier preventing air assault on the palace and with the royal guard present the changelings would not stand a chance in a fight so The Professor sent in Weeping Pegasi to prevent evacuation and heavy forces of changelings in the main city keeping Pinkie busy but WHY, Starlight told me that most of The Professors army was concentrated at the Empire, obviously it's shield would be waaay stronger due to the Crystal heart but everything has a weakness and she would know, so why would Rarity not tell him how to take down the Empires shields if she had switched sides even if she was brainwashed the Empire would have fallen years ago, so can anyone guess why?" everyone sat or stood staring at The Doctor who had completed his rant but no one could answer his question as they could not process how fast he explained.

"Ohh just tell us you time travelling varmint!" Apple Jack yelled as she just couldn't process anything The Doctor said during his rants.

"Oh Rassilon, you ponies are slow, Rarity gave Intel on key targets that I set back up plans for and if she was under my twins control she would have told him everything you girls know, meaning she is still on our side" everyone was still staring at him with blank looks, to which The Doctor just collapsed with a massive sigh.

"But wait Apple Jack was right Rarity wouldn't let any one touch her hair" Fluttershy said revealing that she understood every word The Doctor had said bring his head up with a massive grin on his face.

"Rainbow how long was it before Rarity told The Professor the first bit of Intel?" Rainbow took a moment to think about the question as her mind was still frazzled shaking her head out of confusion.

"Uhh well since our capture I would say three, no four years…wait, Ohh I get it now" Rainbow had realised where the Time Lord was coming from and he stood up still with his trademark grin.

"Four years without a makeover could make a girl like Rarity do anything especially for revenge, because I know how a person under his control acts and in terms of fighting they never spare a life and why shoot Nightmare you may ask, to maintain her cover and to reunite us" this realisation made everyone smile to the fact that this battle may yet be won.

**Rarity's Quarters, same time frame**

As Rarity was excused by The Professor she walked very slowly back to her quarters which (under arrangement) was the only place in the castle The Professor would not go in, since despite being a murderous psychopath he was a man of his word and Rarity enchanted the door to only allow her through but as she walked in most people would expect a gleaming, glamorous suite with everything a girl could want but the truth was far more heart breaking. the entire room was a mess, the dresser burned to ashes, the bed unmade with the pillow soaked, in fact the only thing untouched was the desk similar to the one she had in her room back in Ponyville, she had spared it of her rage as she needed something to make sure her mane was a perfect as ever and as she dropped her sniper rifle on the floor with a loud thud she collapsed on her desk chair and began to cry, it was smart of her to convince her complete privacy in her quarters as if The Professor saw this he would begin to suspect her treachery. On her desk was a brush, hair dryer basic make-up accessories to make her look the way she always looked and sitting alone taped to the mirror was a burnt picture of herself and her little sister Sweetie Belle with the family she had made with that sweet Brown earth stallion and in the picture hugging Rarity's leg making her look down was a little cream coloured colt with the same beanie with the propeller that his father wore as colt in fact even he messed up the photo by putting on a fake moustache making Sweetie Belle the only pony looking at the camera properly, this photo made her laugh and cry as not only was it one of her most fondest memories but it was also only 3 months before the war and Sweetie Belle and her family were killed during the first attack on Ponyville, this made Rarity swear on her life that she would make the one responsible pay for the death of her sister but the involvement of her friends changed her plans greatly, so she had to adapt to the situation and therefore after her daily sob she fixed herself up and took a case from under her bed, opening it was the pieces to something she was given by The Doctor which she salvaged after being let out by The Professor, it was a prototype Anti-material rifle built especially for her. As she had finished building it she took out the foam filling and her eyes sparkled at the majestic beauty that lay before her raising her confidence and her determination of avenging her family.

"IT. IS. ON"

**Holding cells**

"Ok, so we now know that the fool who shot me did so in regret big deal, we are still stuck in here" Nightmare complained as everyone was thinking of a way out while Celestia rested.

"Shut it; don't speak unless it's helpful, in fact I'm surprised you're still around at all, I though you couldn't take over yet" The Doctor said while redressing Nightmares bandage.

"In fact it wasn't my choice to be in control, it was my other half, you see she is aware I exist and her mind is stronger so I can't take over when she is conscious and taking control as she sleeps is too dangerous as she would feel exhausted if I roamed as she slept" as nightmare explained The Doctor was deep in thought.

"So you are not connected in the sense you need Luna to survive?" he asked while looking out of his cell and down the halls.

"No, if one of us where to perish the other would survive" as The Doctors head dropped he realised he had no choice.

"Well then I have a way out and a victory plan" everyone got up to listen but by the sound of his voice, he personally didn't like it "but first I'm going to over you an alternative place to reside"

"And where would that be Time boy?" she asked unconfident in his words.

"My mind" this made everyone even Celestia who had woken up gasp in shock, it was apparent that The Doctor wasn't fond of Nightmare but to allow her to enter his mind was another level of crazy "it's a lot bigger than almost any pony you'll come across, though you wouldn't have any control, I'll promise to put you in your own body as soon as, then I will take you anywhere you want to live out you little fantasies and everyone ends up happy" Nightmare and The Doctor stared at each other while everyone else looked at each other then at the Time Lord standing before the Mare of Darkness.

"But Doctor that's a terrible idea is it even possible?" Twilight showed her concern for her friend's safety but The Doctor had made up his mind he was just waiting for Nightmares agreements.

"Why? Why would you allow me to enter your mind?" The Doctor leaned in closely at nightmare and spoke quietly enough for only her to here.

"you know something about me, from when we first met you didn't notice Twilight walk right past you and for a brief second you were afraid, not of the elements but of me, why?" this made Nightmare laugh revealing the jagged teeth that formed from her transformation.

"at the moment you can't feel it but Unicorns and Alicorns can sense magical energy and when you blathered on about you're many victories you're magical level raised even higher than 'Princess' Sparkle and to my understanding not even Celestia's nor Luna's magical energies has even come close to Twilights full potential, she may not be able to control it even now but it's there just as it was when we all met and for a brief moment you overpowered your own roommate whose very talent is magic. Makes one think Doctor" it made little sense to the others but to Celestia, Nightmare and the Doctor the pieces connected perfectly.

"I did some tests on the energy that allows me to regenerate and compared it to your magic, I discovered that my regenerative energies give off high amounts of magical energy and my body used said energy to morph me in to a pony mimicking the process of regeneration yet still allowing me to keep my personality and some features like eye and Hair colour but you have the skill necessary to beat The Professor and I know how he thinks, if we combine our skills and strategies we could beat him in one blow" everyone listened in to Nightmares answer which was surprising to say the least.

"Very well, I accept" and with that the doctor pulled out a phone from the little bag he had and began talking thought it.

"Rarity, it's me The Doctor" Pinkamena raised an eyebrow confused by The Doctors actions.

"Oi, pin head, she won't have a Phone on her!" Pinkamena yelled wishing she could hit I'm across the head.

"Who says I'm calling at this exact moment. Hey Rarity I need you to pick up something from Canterlot"

**30 minutes later**

"Right that's that set" The Doctor said while putting his phone away.

"Care to explain" Rainbow asked as The Doctor looked down at the stairs leading out.

"Don't worry everything will become apparent in three, two, one…" after counting down everyone began looking at each other making Rainbow smirk at The Doctors Failure.

"Wow that explains everything" she said slowly and with her usual sarcasm.

"no, my watch must be slow" as he began shaking his pocket watch which he kept under his tie, several guards fell down the stair with bullet holes in the centre of their heads "ahh there we go" now happy with his handy work Rarity walked down the stairs blowing at the silenced magnum attached to her hoof on her back was a large rifle, bigger than the last and a fairly large Sword which seemed fairly familiar to Twilight and Celestia.

"Is that the sword of time?" Celestia asked recognising the blade and remembering its keeper "oh…Light Bringer it's been so long"

"Who's Light Bringer?" The Doctor asked wondering who the sword that was apparently his reminded the princess of someone else.

"Just a pony that was very close to me" Celestia explained while trying to get up stumbling in the process.

"Well I'll be glad to meet him someday or year" he said forgetting the pure white murderess standing behind him.

"Do you mind? This giant tooth pick is incredibly heavy!" now focusing on his plan, The Doctor walked up to the cell door and plucked off one of his feathers.

"SHIT! DAM THAT BLOODY HURTS! Never doing that again" using the feather to try and unlock the door a familiar black and silver device fell on his head and broke his concentration but he had noticed it was incredibly old "my screwdriver, how did?" looking around he saw Twilight giving him that smile that told him she had his back along with the rest of the gang and with a twirl and a buzz the doors unlocked letting everyone out "I don't know how or why you had this or in the condition it's in but thanks Twi"

"You're welcome Doctor" Twilight said giving her first friend a hug "but it wasn't me who had it" she said braking off and Twilight turning to Pinkamena, who was currently walking out of her cell while combing her hair.

"Pinkie?..." Pinkamena put her comb away and walked towards and also gave The Doctor a hug and whispered something into his ear preventing the others form listening.

"You listen her Doc, you are one of my best friends and we have all changed since that day but you changed years before, you became cold, darker, every bad guy we faced we ether banished or destroyed because of that we all lived in ignorance, we never stopped to notice what the future held but for all that time you feared for the worst. So when you go back to the Past Promise me one thing" The Doctor did not know what to say as he had no idea what this experience would have done to him but like The present Doctor of this time he knew he had no choice "don't lose that smile" with Pinkamena braking off from The Doctor he saw every friend he made so far standing before him and he knew he had to end this and it was about time he did too.

"Thank you Pinkie, RIGHT! Everyone stand back this may get explosive…I do express the 'may' Twilight over here" The Doctor ordered pushing everyone to the wall with Rarity using her magic to support Celestia as she walked along with The Doctor waving Twilight over.

"Wait didn't you just ask us to move back, what do you need me for?" The Doctor hoof smacked himself.

"30 years, 30! And she still questions my logic" he mumbled to himself before pushing Twilight over to Nightmare Moon and handed her a piece of paper "I need you because I require legal authority and you are a princess plus Celestia isn't up for it, now read that" as Twilight over read the piece of paper she blushed at what it actually was.

"Doc…Doctor this is a…" The Doctor actually hit his head on the floor as result of Twilights reaction.

"Watch that head, what do you expect me to live in if you keep hitting it" Nightmare said with a giggle as like Luna she found The Doctor funny when he was agitated.

"Twi, I know what it is just read it before I change my mind" both Twilight and The Doctor exchanged a look of trust and she began reading the paper aloud.

"Princess what is that?" Rarity asked Celestia to shed some light on what was going on.

"It's a true matrimony spell" the five ponies surrounding the Princess of the Sun all screamed in reaction to her answer.

"WHHAAATTT!" they all screamed in unison.

"Oi! Girls keep it down over there" The Doctor shouted in order to let Twilight concentrate.

"Unlike a normal matrimony, the people to be wed are bound by a belief, this kind of matrimony binds two minds into one body" Celestia's explanation didn't help the confusion but it did clear a few things.

"Oh so that's why The Doctor offered Nightmare Moon a place in his mind" Fluttershy said understanding the Time Lord after Celestia's explanation.

"That is correct Fluttershy, now let us hope that binding the two minds together can save us all" the six remaining ponies sat back and watched as Twilight recited the incantation.

"Nightmare Moon, do you wish to enter The Doctors mind, in order to find Peace and enlightenment?" Twilight looked to Nightmare Moon curious to her response to see if she was lying but if she wanted control she had to knock down the fools who had it.

"I do" she didn't have to say it like that but she did and it made The Doctor even for anxious about letting the being in front of him enter his mind for who knows how long.

"Doctor, do you permit Nightmare moon into your mind, in order to find peace and enlightenment?" it was now time for the final confirmation and it took The Doctor a good minute to think about it.

"I do" and before Twilight could finish the rest of the sentence, two bright lights began to emit from both Nightmare and The Doctor, Nightmares being Blood Red and The Doctors being very Royal Blue or Tardis blue as he liked to call it and as both lights flickered like a flame the both came together into a dark shade of purple and from there the purple fire engulfed The Doctor and died Down followed by the collapse of both Nightmare and The Doctor.

"The ceremony is complete" as Celestia reassured the rest that everything was over Nightmare moons eyes began to flicker as her coat and man returned to normal.

"Hold on I thought, nightmare put her mind into The Doctors so why is she waking up?" Rainbow questioned due to the fact she was not present during the transformation but when her Nightmare Moons eyes opened, they were not the cold slits of the mare of darkness but the warm teal blue eyes of Princess Luna.

"Oww, my head, what happened? AHHH!...what the? I'm bleeding" it was clear that Luna was going to have a nervous breakdown but nothing anyone could think of could work however Twilight remembered The Doctor taught her a trick to put someone to sleep.

"Princess, calm down your going to be fine but you need to rest" Twilight assured her but it had little effect.

"Like hell I need to calm down where is The Doctor?" and just before she could see him on the floor Twilight used The Doctors trick and placed pressure on a certain area making her fall instantly to sleep laid up against the wall.

"Well at least we have Luna back to normal, am I safe to assume it's only The Doctor and Luna that came from the past" Twilight was hoping from a conversation about what they would become but Celestia raised her hoof to stop her.

"I wouldn't, my sister may not hear us but The Doctor will most likely remember what we say" and as though reacting to her statement, The Doctor rose and though his coat was grey it was noted that he was getting darker along with his hair which was turning silver and standing on end.

"Doctor?" Twilight walked slowly towards her old friend but took a step back as when he opened his eyes, they flashed bright white.

"No more…" he spoke very quietly making the girls and princess wonder what he was saying.

"What was that you said?" Twilight asked again but she had noticed that the dirt and hay at his feet began to move and gold light began emanating from The Doctors body but as the force died down The Doctors eyes returned to normal.

"Sorry what?" he said as his ears flopped up and down like he was adjusting them somehow.

"You said something, what was i?" Twilight stared at The Doctor but all she got was the 'I know what you're on about but I don't want to talk about it' stare.

"Not important" The Doctor said quietly before turning to everyone else "Right anyway, plan is…" before The Doctor could explain his plan Rainbow Dash butted in and presented her idea.

"Me, Pinkie and Apple Jack blast thought the guards leading up to the throne room, then Twilight and Rarity suppress The Professor from afar then you fly in and finish it with a final one on one battle to the death" when she had finished everyone in the room stared at her somehow surprised she came up with a good plan.

"Excuse me, who's in charge?" The Doctor said as he had not presented his plan.

"Sorry, what do you have in mind?" she said with her usual tomboyish attitude.

"Right!, here's the plan" The Doctor said facing the exit to the dungeon then he turned back to Rainbow Dash with his goofy grin "like ya said, nice plan" then he focused his attention to everyone else "any questions?"

"Yes, just one what do I do?" Fluttershy asked as she was not mentioned in the plan Rainbow made.

"Right, yes forgot about that, Celestia can you walk on your own?" among all the craziness of the last few minutes Celestia had gathered the strength to stand reliving Rarity the need to hold her up.

"Indeed, I can use my own magic to assist" now with Celestia's mobility sorted he turned to Luna.

"good, she isn't awake, no telling how she would react" The Doctor in his hyper active mode while quickly moving to Fluttershy "Fluttershy how strong are you?" he asked looking over her body before somehow placing the unconscious Luna on top of her, nearly making Fluttershy's knees buckle but she held "good you carry Luna, then you and Celestia just follow the chaos"

"Can we go know? I'm itching to bust some flank" Rainbow asked becoming impatience.

"Yea, yea fine go, I'll catch up" it didn't take long for the girls to rush out but as The Doctor walked towards the staircase he took a moment to look back at Luna unconscious on Fluttershy's back.

"You really care for her don't you?" Celestia commented after noticing The Doctor take a moment.

"Is it that obvious?" The Doctor replied calmly still staring at Luna as she slept.

"from her definitely" she said with a giggle as Celestia could read her sister like a book, the thought of which brought back many memories from the past 30 years but then her emotions dropped while she looked at the Time Lord who was now facing the staircase leading out of the dungeon "we had this conversation 30 years ago and what I said then personally is the best time to hear it. Right no you need to end this and bring peace back to Equestria!"

"Yes ma'am" The Doctor took another moment to think of a battle plan but he knew The Professor could counter it just as he could counter him.

"_It's nice and cosy in here, very spacious, i should order some furniture"_ The distorted voice of Nightmare Moon echoed in The Doctors head as he thought and in the span of a second both Time Lord and Mare of Darkness could engage in a full on conversation.

"_**Shut it, you're in there to provide attack strategies not to comment on the inside of my brain!"**_ The Doctor raised his mental voice as he could hear Nightmare Moon literally as a voice in his head.

"_very well, party pooper just go and fight him and I'll influence you're movements so he can't counter you" _The Doctor opened his eyes and rushed forward and flew up the stairs grabbing The Sword of Time as he flew, it was surprising not only had Nightmare moon entered The Doctors mind he could feel a difference in his speed and strength, though that was not on his mind as his goal was in reach and just as he over took his friends clearing the path, The Doctor burst through the doors and into the throne room where The Professor was standing spear in hand and in the split second of entering the large room both Sword and spear clashed.

"Heard you had a party downstairs and you didn't invite me!" The Professor took the upper hand and forced The Doctor back keeping himself up with his wings.

"_Dang it! It had no effect"_ The Doctor thought to himself and in turn Nightmare Moon, who had a big smile on her face which The Doctor could not see.

"_**Sorry time boy but I lied when I said I would influence you, I doesn't work that way, yes you may have a slight performance boost but only I can control my own power!" **_The Professor hesitated as he noticed another mind.

"oh Doctor you disappoint, teaming up against little old me, well _SHE WON'T SAVE YOU!_" it was unclear how The Professor could hear Nightmare or even notice her but as he swung his spear he unleashed a wave of magic basting The Doctor back knocking him out of the air.

"_Nightmare you are not getting my body!"_ The Doctor spoke directly to nightmare who was just laughing her head off.

"_**well then, you lose and everyone even you're precious Luna will die…just give me shared control and you may have a chance"**_ Time seemed to slow down as The Doctor thought about his decision, he knew he had no choice but he had to be sane enough to get Luna home, maybe that s when the future Doctor comes in but whatever the end case, The Professor must be stopped.

"FINE! YOU WANT CONTROL THEN TAKE IT!" The Doctors uproar shook the ground causing The Professor to stop and get his footing and as he looked at his foe, he saw something that he never though The Doctor would do. Black smoke enveloped the time lord, his eyes turned to slits coloured blood red, his coat turning a void black, his hair silver and which followed was a cold yet calm laughter which The Professor recognised "control finally!, it's good to be free!"

"Let me guess, Nightmare Moon?, using The Doctors body won't give you the upper hand my dear" The Professor spoke calmly holding back his usual blood thirsty self but The Being in front of him was no Doctor and certainly worse than a nightmare.

"Nightmare Moon? That weakling was only the catalyst I needed to gain control. Funny isn't it the one thing I needed was in another universe and now I have what I want and The Doctor is no more!" The professor could see that this was not his nemesis nor the dark mare from before but there was a familiar atmosphere coming from this new acquaintance.

"You! so this is why you let me out...to use me!" The Professor had put the pieces of the unknown pony that let him out of the black hole prison.

"well, i certainly don't know what you are going on about but thank you for telling me that 'Professor'...but who am i?" the dark stallion walked around getting a feel for his new found control "even if i kill you, calling myself The Professor is just wrong, he was the 'hero' you are the mad one, i myself prefer that mastermind feel, what do you think?"

"Why does it matter?"

"Well, a Time Lords identity is just as important as his name...remember father's trial when he was in his sixth incarnation, i like the name of the accuser, what was it...Valeyard, _The_ Valeyard! Perfect!" as The Valeyard (as he now calls himself) declared his existence the rest of the gang with the exception of Celestia, Fluttershy and Luna, entered the throne room shocked to see The Doctor not trying to fight The Professor.

"Doctor! What the hell are you doing! GET HIM" Rainbow Dash shouted unsure why The Doctor had not followed the plan without knowing of the control switch.

"Do not tell me what to do you inferior piece of trash!" the gang was shocked to hear the eldest of their group say such a horrible thing; this gave Twilight the message that something was not right.

"Doctor, why would you say such a thing?" The young princess said as she walked towards the form of her dearest friend only for him to move very quickly to her ear whispering.

"_I'm no Doctor, i am darkness incarnate"_ Twilight frozen in place, she and her friends could not stop The Valeyard's next move, as he moved towards Twilight he had moved again above her Sword in hoof and aimed for her neck "Be gone Twilight Sparkle!" and thinking it was her last moment and at the hands of her trusted friend she was pushed out of the way and The Valeyard's attack was blocked by The Professor.

"you where the one who let me out AND I THOUGHT WE WHERE ON THE SAME SIDE!" and summoning all the strength he had The Professor pushed back The Valeyard and both Time Lords would have their battle "now i see why you asked me to fight The Doctor, i can also see my foolishness for listening to you!" The Professor had unleashed an extreme amount of rage as he continued to strike The Valeyard "i was desperate to get out and YOU USED ME!" it appeared that The Valeyard was not prepared for this fight as he struggled to move and all he could to was deflect but he was a quick learner as when he did get a chance to strike he cause serious wounds on his opponent.

"i quite like hearing about me, i sound exciting" The Valeyard may have only been using The Doctors body for the span of a few minutes but his intellect was by far greater when it came to strategy, proven by the fact he was untouched and his opponent was bleeding heavily as he fell in a pool of his own blood.

"The one time i route for the bad guy, he has to lose!" Pinkamena shouted as The Professor fell to his knees while Celestia and Fluttershy entered (with Luna still asleep yet slightly stirring from the commotion)

"Doctor, forgive me" using what every strength he had left The Professor used the little magic he had to throw his spear hopping to pierce The Valeyard but having lost a lot of blood his aim was off and The Valeyard was able to dodge it only having his tie caught and torn off and as The Valeyard laughed at the feeble attempt to kill him but looking down he stopped at the sight of the Tartan tie torn on the floor and from across the room a certain lunar Princess began to open her eyes and see the stallion she tried to save caught in the same darkness that once consumed her.

12 hours ago

"so Doctor tell me, where did you get that tie, i have never seen a pattern like it" Luna asked as The Doctor and The Princess had been getting to know one another over the course of the Grand galloping gala.

"Huh? This old thing, it was a gift from an old friend of mine and i wore it everywhere i went sort of like my symbol, the man with the tartan tie! And i was lucky it survived the crash a few months ago as all my other clothes were ruined" The Doctor explained while staring at his tie that looked very old almost matching his eyes in age "if this thing was every ruined, it would be heart braking, double count in my case"

"Huh?" Luna asked confused by his last comment "what do you mean by double count?"

"i have two hearts, no big deal" as the memories flashed back to reality Luna stared at The Valeyard as he turned to face The Professor, raising his blade to strike, causing her to jump from Fluttershy's back and attempt to stop The Doctor under the control of the darkness.

"DOCTOR! STOP!" the sound of Luna's voice echoed through out the castle and The Valeyard dropped his arm ceasing his execution of The Professor "Doctor, i understand what its like to seek revenge but there is no need to kill someone for it, you told me that and i was shocked to see that your first thought was to kill him, please just don't kill him" Luna was on the verge of crying but she had no idea the impact the darkness had on the Time Lord. The Valeyard turned with a soft expression on his face that only The Doctor could pull but it all washed away when his expression turned to anger.

"how dare you speak to me like that, you will be silent" in that instance he sped over to Luna and went to strike her, Celestia rushing to her sisters aid but he did not move, he couldn't move a muscle "i can't move! Professor release me!" but as he managed to turn his head the professor was still on the floor bleeding and non of the unicorns nor Celestia was keeping him still, in he had lost control.

"_get out" _the voice had come from the same mouth but it was by far not the same person and as The Valeyard and the other fought for control gold energy began to emit from The Doctors Body.

"It's mine now!" the Valeyard yelled before the gold light consumed the body.

" .IS NOT!" and in a flash The Doctors body erupted in an explosive gold light and in that instance two bodies were shot out to ether side of the room. One was The Doctor with his grey coat and messy hair while the other was the same dark stallion.

"NO!" The Valeyard felt his chest and discovered something he did not like, while The Doctor stood across from him breathing heavily.

"No one threatens her...NO ONE!" as The Doctor had raised his voice, shockwaves began to shake the floor and his eyes where shining bright white. And for the first time 200 years The Doctor was furious "No more!"

TO BE CONCLUDED

Next Time:

Rewind

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	12. Episode 11: Rewind

Doctor Who:

The Equestrian Chronicles

Episode 11:

Rewind

"DOCTOR! STOP!" the sound of Luna's voice echoed throughout the castle and The Valeyard dropped his arm ceasing his execution of The Professor "Doctor, I understand what it's like to seek revenge but there is no need to kill someone for it, you told me that and I was shocked to see that your first thought was to kill him, please just don't kill him" Luna was on the verge of crying but she had no idea the impact the darkness had on the Time Lord. The Valeyard turned with a soft expression on his face that only The Doctor could pull but it all washed away when his expression turned to anger.

"how dare you speak to me like that, you will be silent" in that instance he sped over to Luna and went to strike her, Celestia rushing to her sisters aid but he did not move, he couldn't move a muscle "I can't move! Professor release me!" but as he managed to turn his head The Professor was still on the floor bleeding and none of the unicorns nor Celestia was keeping him still, he had lost control.

"_get out" _the voice had come from the same mouth but it was by far not the same person and as The Valeyard and the other voice fought for control gold energy began to emit from The Doctors Body.

"It's mine now! It belongs to me!" the Valeyard yelled before the gold light consumed the body.

" .IS NOT!" and in a flash The Doctors body erupted in an explosive gold light and in that instance two bodies were shot out to either side of the room. One was The Doctor with his grey coat and messy hair while the other was the same dark stallion.

"NO!" The Valeyard felt his chest and discovered something he did not like, while The Doctor stood across from him breathing heavily.

"No one threatens her...NO ONE!" as The Doctor had raised his voice, shockwaves began to shake the floor and his eyes where shining bright white. And for the first time 200 years The Doctor was furious "No more!"

**Conclusion**

"Doctor?" Luna asked the grey stallion while still aching in pain of her bullet wound "are you the Doctor?"

"Luna stay back, then we can go home" The Doctor said calmly but The Valeyard began laughing maniacally.

"Home! You're not going anywhere with that body, it belongs to me!" The Valeyard shouted across to the good man he was born from.

"SHUT IT! you may have been in control but I saw and heard everything. I always despised The professor for what he had done but now I see that he is just what I would have become if I let you out of the cage, so now I'm going to take down the real murderer that killed Willow…YOU" now sure The Doctor was going to attack The Valeyard shot for the Sword of Time as it was dropped before the separation but before he could touch it, the blade lifts and throws its self towards The Doctor, catching it The Doctor opened his wings, and with the rising sun shining from the window behind him he would have been mistaken for The Keeper of Time so long ago, he shot towards The Valeyard with such speed it took a moment for everyone to process the attack. The Doctor stood on his hind legs in the position of someone after the swung a sword then blood burst out from The Valeyard face.

"ARGHHHH!" The Valeyard fell to the floor screaming in pain, covering the left side of his face still able to see with one eye "DOCTOR! YOU WILL PAY FOR THIS!" while The Valeyard continued to scream in agony, The Doctor lowered his Sword and let his wings drop.

"I already did" he said quietly to himself, then suddenly he was tackled to the floor by a certain teary eyed princess "ahh Luna!"

"I'm so glad you're alive, I don't know what I would do without you" everyone apart from the other too Time Lords bleeding on the floor smiled to the fact that the war was finally over and The Hero's from the past were reunited an ready to return home.

"Well if you keep hugging me you may find out…_can't breathe_" The Doctor replied being crushed under the pressure of Luna's Hug of death but The Dark stallion rose behind the Time Lord still holding the left side of his face and holding The Professors Vortex manipulator.

"You have one this day _'Doctor'!_ But know that we will meet again…and that day will be your funeral" The Valeyard activated the device and was gone from this time.

"Well looks like we'll be seeing him again" The Doctor commented before turning back to Luna "but more importantly I'm glad you're safe Luna"

"May I ask Doctor, who was that stallion?" Celestia asked referring to The Valeyard.

"I don't know, my inner darkness I suppose…BUT we have to fix this world, no sense leaving it in ruin" The Doctor added with his cheerful grin.

"What do you mean Doctor?" Luna asked unsure of what he was going to do.

"You brought the elements didn't you?" Twilight said having known more than most, how the doctor thinks.

"Yup! Well actually I'm about to ask starlight to bring them" and on cue a bright light blinded the entire room and Starlight along with Harmony and Quantum "ah right on time "hi kids!"

"You never change Doctor" Twilight said while shaking her head in embarrassment.

"I was expecting a fight, anyway Doctor we brought the Elements from the everfree forest but we only have 6 of them" Starlight said handing The Doctor a chest filled with the elements.

"no worries, I have it here" The Doctor assured Luna's eldest holding up the long blood stained blade, as Starlight looked around he saw Rarity and Rainbow dash alive and well and he also saw someone he missed dearly.

"Aunt Celestia" Starlight shouted like a little kid as he ran to her giving her a long awaited hug "I'll so glad you're still alive" Harmony also went to embrace her aunt leaving Quantum sitting there.

"How old are you Quantum?" The Doctor asked the young colt

"Twelve" he said a little saddened.

"So you must not now who Celestia is then"

"My parents told me how wonderful she was but I never got to meet her" The Doctor then got up from Quantum's side and patted him on the head.

"well theirs your chance" giving The Doctor a big smile Quantum ran towards the aunt he never met but before that he turned back to give The Doctor a hug first.

"You remind me a lot about my dad, thanks for helping us" The Doctor smiled at this little colt as he ran off to be with his siblings, he then turned to see his old foe bleeding on the floor.

"You need a hand?" he asked expecting The Professor to be still alive.

"You're an ass but I could do with a drink" The Professor replied attempting to get up still bleeding.

"Are you going to…you know?" The Doctor asked talking about regeneration.

"No I'll live, so what about us?" The Professor said unsure of how the two Time Lords will interact from now on.

"no idea, might leave you here, let you answer for your crimes or I can take you somewhere for you to have a life" The Doctor replied before opening the chest containing the elements.

"So Doctor what are you going to do?" Twilight asked picking up her Element crown form the chest, and then The Doctor started placing the elements on each of his friends respectively.

"Well we know that The Elements purify evil and disharmony but that only requires 6 of the elements but combine all 7…" he began to explain before standing in the middle of Rainbow Dash, Rarity, Fluttershy, Apple Jack, Pinkie and Twilight "we have a magic Time Machine"

"One problem, the Elements won't work if we are selves aren't in sync with them" Fluttershy mentioned making everypony look at Pinkamena.

"What!? Their nothing to laugh about" she said taking off her element.

"Well then you leave me no choice, sigh Twilight I'm sure I gave you one?" Twilight using her magic brought a small wooden box and gave it to The Doctor; opening it The Doctor pulled out a photo and showed it to Pinkamena.

"wha?…wha!?..." after processing what she was looking at she eventually burst out laughing making her mane frizz up back to normal. The Doctor then put the photo away and gave the box back to Twilight.

"Doctor what was that?" Luna asked as she noticed Pinkie was pointing at her while she laughed.

"you're foal picture" He replied calmly before signalling everyone to activate their Elements.

"Ohh…wait? WHAT! DOCTOR!" Luna yelled at the Time Lord as he used His Sword to harness the power of the elements and then as his eye glowed white like they did when he attacked The Valeyard, the world around the large group began to move like time was going backwards, starting off slowly but increasing in speed. As it did so wounds began to heal, Luna's bullet wound healed, Celestia's strength returned and her hair grew and returned to its normal colour and the cuts and gases on The Professor healed also. So many days had been taken back and when time slowed to a stop The guardians of Harmony, Luna, Celestia, Harmony, starlight, quantum and The Professor where all standing in a field, the same position but with no castle. As The Doctors eyes returned to normal and the deed done, the elements turned to stone and the necklaces dropped to the floor along with The Doctor.

Opening his eyes The Doctor vision adjusted to reveal Luna, who had caught him as he collapsed.

"Hi" The Doctor said awkwardly as they were both in the same position back at the palace only their roles reversed.

"hello" Luna said with a giggle helping The Doctor to his feet and as he looked around everyone was there, even the TARDIS.

"Ah! that's my girl, following the temporal alteration and recognising it was me" The Doctor explained The TARDIS's appearance without prompt

"What did you do anyway?" Twilight asked on behave of everyone else

"I rewound time" he said picking up The Sword of Time

"You did what?" Apple Jack asked not getting what the Time Lord meant

"I rewound time, we are in the same position 10 years in the past" The Doctor explained before he stuck the sword in the ground

"what!?" everyone exclaimed wondering why would the crazy madpony take them back to before the war

"Don't worry the war won't happen now, to put it in a better term you aren't 10 years in the past but the past is ten years in the future, that's why young quantum here isn't 2 years old" The Doctor further explained ruffling Quantum's mane

"But why would you do that?" Harmony asked knowing The Doctor would only do this for a good reason.

"You all lost something in that war, I may not seem it but I'm highly observant, first no Celestia big red flag no one mentioned her till after he saw her armour gone, Pinkies attitude she only pulls her hair staright when she has been mentally hit, right?" The Doctor said asking pinkie who was now just about back to her usual self

"Right!" pinkie shouted agreeing with The Doctor but in truth she wasn't sure what he was saying

"Apple Jack you lost Big Mac, that's the reason you were on the frontlines, Fluttershy…I'm actually not sure about you but I'm guessing it made you more confident, Rainbow Dash you lost the pony you loved, don't ask I know I've been there, Rarity you lost the one person you truly cared for, your little sister which is why you began so tolerant of the thing the past you would never do and finally Twilight…the war itself tore your heart open and you couldn't bare it, again I know what that feels like" The Doctor had revealed what he had noticed about the future versions of his friends and had taken steps to fix it "that's why I've rewound the clock, everything but the ponies who stand here have been reset, those that have died are no longer dead, split families and political alliances reunited" The Doctor began picking up the speed of his words as he stood on a cliff overlooking Equestria "JUST THIS ONCE EVERYBODY LIVES!"

"Sweetie belle is alive!" Rarity trusted The Doctor an knew he would never joke about that, she was so overjoyed she began crying, even Apple Jack shed a tear as she looked at the picture of her big brother who to her had died years ago.

"Thanks Doc, I never doubted you for a moment" The Doctor turned to face the group of ponies that had/ will help change his live and then decided to leave

"Of course of course, now run along I've got to get this princess home its past her bed time" his witty comment earned him a whack over the head by the Princess of the night "ow! Hey its morning isn't it"

"I know, that was for showing Pinkie my foal picture" The Very mention of it shot Pinkie into a laughing fit followed but a comment from Celestia

"You can't blame him sister, it was a very funny picture, and I should know I gave it to him" Luna had blushed madly before trying to attack Celestia but failed miserably "maybe you'll get me when you're older" Celestia then whistled causing the Tardis doors to open, shocking The Doctor

"Wait WHAT!?" looking into the TARDIS making sure it was his he almost got his head taken off when Luna flew past her

"I'll get you one day Tia, ONE DAY!" as the door shut then locked (suspiciously) The Doctor then turned to face The High Princess

"Thank you, Doctor once again for everything" The Doctor then turned to face the TARDIS and was going to leave without saying a word "aren't you going to say something"

"What is there to say, bye I'll see you in five minutes, you should know by now I'm not one for goodbyes" The Doctor said looking back

"Of course but remember that you will always have someone to help, especially my sister, farewell Doctor" The Doctor waves Celestia good bye as he entered The Tardis Spotting a very fed up Luna, after walking to the console he set the coordinates and launched the Tardis

"Who was he? The Valeyard" Luna asked while The Doctor flew the Tardis

"we was my version of Nightmare Moon, both fuelled by darkness and our negative thoughts, yours of jealousy and resentment, mines of anger and blood lust from the war" The Doctor replied not looking up from the controls

"And my dark half, Nightmare moon"

"No idea, suppose she bonded with The Valeyard or is still in here somewhere" The Doctor guessed pointing at his head "but ether way, we will see them both again. Now then we need to get you home, better get back in your gala dress" The Doctor instructed before checking his tie only to remember it was ripped off.

"Do we have to go back to the gala?" Luna asked with a moaning tone of a little filly

"What are you five, you have to be there it's the first Gala since you returned, we don't have to return at the exact moment we left, I just think you should be there to greet the guests or something pony related"

"But I remember the Gala's from before being so boring and tradition is a big thing with the event, it will just be full of posh ponies that only show respect for our position not for who we are"

"ok, I see you're point we don't have to if you don't want to but I do say a day with normal live will freshen you up, and trust me on that it's the curse of travelling in a tardis, you begin to long for the normal life" The Doctor continued as he walked down one of the corridors out of the control room getting quieter as he moved further and further away, then Luna jumped when The Doctors voice came from the console _"I would still put your gown back on"_ Luna looked at the monitor and it read the exact date of the gala but a full 3 hours after they left

"Typical" reading the other details on the screen it also said ETA was 30 minutes "well might as well freshen up then" and Luna walked toward the Tardis washroom to face her greatest foe…The Shower

**20 minutes later**

After spending longer than she wished getting washed she was finally back in her Gala gown and had re-entered the control room witnessing The Doctor eating a sandwich filled with cooked pink slices

"what is that in your sandwich?" she asked with genuine curiosity

"bacon, never mind that, do me a favour and pull down a small lever with a yellow handle" looking over the console Luna found a series of small lever most with red handles, two with blue and one yellow, after she pulled it the noise the Tardis made while in flight stopped and with a light thud the ship stopped entirely

"What did I do?"

"You turned the cloak, so you can sneak back in to the party unnoticed also I don't trust the guards that much with my old girl" The Doctor then turned to Luna and set a few more controls before landing

"Doctor, I need to talk to you about something" Luna asked hoping to get a matter out the way before she left The Tardis

"The moment before Nightmare regained control" The Doctor said, revealing he knew she would mention it sooner than later "I'll be honest with you Luna"

"You don't feel the same way" Luna said expecting the very thing

"That's not what I'm saying, you matter so much to me and I can bare to lose you but…I don't think I can do a relationship like that at the moment, I'm just not ready" The Doctor said as both Alicorn and Time Pegasus stared at each other "I'm 464, to Time Lord that's like late teens and the Time War was only 100 years ago for me, I lost so much, most of my family, my friends, my Fiancé" that word hurt Luna slightly as The Doctor revealed he had someone else in his hearts "I'm sorry Luna, I hope to be able to see you as that kind of person but I need to let go of my pain first and that will take some time" Luna's face dropped in embarrassment and sadness, she had fallen in love and she still thought he didn't return her feelings

"I'm sorry Doctor, I didn't know" The Doctor walked up to Luna and brushed her hair to reveal her beautiful teal coloured eyes

"give it some time" and in the moment which felt like an eternity The Doctor locked lips with Luna and she could feel what the Doctor actually felt for her and as they broke apart she told herself she could wait

**Jo's Donut store**

Being dropped off in her room Luna decided to go and look for her sister but as she walked around nobody had seen her and the ball room was a mess, she thought of many places Celestia could go to and remembered Celestia bought her donuts for her first piece modern food and remembered a donut store not too far from the palace. As she walked in the store she saw the female majority of the Guardians of harmony and her sister conversing around a table while enjoying several packs of donuts

"there you are sister I was wondering where you had gone" Celestia turned round to see Luna in her gala gown.

"ah Luna did you enjoy your little adventure with The Doctor" memories from back on the tardis cause Luna to blush but she kept her composure and sat down to join her friends

"oh course it was quite thrilling better than some silly gala" Luna was of course Lying, she had been terrified and by mourning when she would go to bed, she would lay awake thinking of that future and who was the father to her future children

**Back in The Future: 1 week later**

Under the circumstances Celestia gave The Professor a pardon for causing the war and he himself spent the last week travelling across the world and learning about the ponies he lived among. Every morning he would spend his time drinking a cup of coffee and watched the sun rise, as he did so he thought about his life and all the wrong he did.

"Excuse me sir would you like another coffee?" a blue unicorn asked causing The Professor to look up and marvel at her beauty

"yes, thank you" The Professor picked up the cup and handed hit to the young mare

"you're welcome sir, may I ask what brings you to this corner of Equestria" The Young mare was very curious and it reminded The Professor of the onetime both he and The Doctor had in common their child hood

"I'm looking for a place to call my own"

Next Time:

The Doctor and the Crusaders

Remember to check my social pages for regular updates and to ask any questions you may have.

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	13. Episode 12: The Doctor and The Crusaders

Courier: Hi guys I'm back enjoy the episode and remember to leave your thoughts in the review section.

Doctor Who:

The Equestrian Chronicles

Episode 7:

The Doctor and the Crusaders

**Tardis library**

It's been two weeks since the gala and The Doctor spent most of his time modifying the Tardis to suit his pony stature and was currently restocking the Tardis Library using the income he receives off of Celestia, buying every book published. The Doctor had been gone some time by his point of view and was currently parked by the Ponyville play park, which he regretted due to the children spraying on the blue box exterior.

*RING RING*

"Hello this is Tardis pizza delivery, how may I take your order" The Doctor jokingly answered the phone hanging from the edge of the door.

"_My dear Doctor, how are you?"_ The Doctor froze up upon recognizing the posh accent.

"Rarity? What is it this time?" The Doctor had given each of his friends a telephone linked directly to the Tardis in case he was needed but not around but Rarity had made a habit of asking The Doctor a bunch of favours that only a time lord could do, like nip back 10 years and pick up a dress or run to the future and get the latest trend. Of course Rarity never misused the benefits of time travel…mostly but The Doctor was getting tired of doing errands for Rarity.

"_Listen Darling, I have a few errands to run…"_ before Rarity could finish The Doctor immediately intervened.

"Oh no, not this time, I'm a Doctor Rarity not your personal Argos" The Doctor was about to put the phone down before Rarity mentioned something The Doctor wished she had forgot.

"_Doctor you still owe me for your suit" _though he could not see her, The Doctor could sense the smugness.

"Name it" The Doctor replied scratching his head.

"_Like I was saying I need to run some errands in Canterlot and I won't be back till next week"_

"Go on" The Doctor prompted the fashionist.

"_I need somepony to take care of Sweetie Belle"_

"You want me, a 400 year old stallion to take care of your little sister…" an extended moment passed, with only the Tardis internal sounds being heard.

"_Could you?"_

"Sure why not, you go on and scamper. I'll pick her up from school" The Doctor seemed a little too eager but anything to beat Rarity's usual requests.

"_Oh thank you darling, I'll leave a bag for her by my front door" _and on that Rarity hung up the phone and The Doctor proceeded to the control room.

**Ponyville Elementary**

For all ponies age of 7+ must go to school till they reach the age of 12 and have a cutie mark, if not till 17. Like in The Doctors universe school was a long boring session of basic education and Sweetie Belle had fallen asleep in class due to this boredom

"Sweetie Belle please wake up, this is a learning environment not your bed room" the teacher for Sweetie belles class Miss Cheerilee noticed Sweetie Belle asleep and her address of the young filly caused her to shoot up

"Sorry Miss Cheerilee, won't happen again" Cheerilee had also noticed Apple Bloom and Scootaloo also slightly drowsy and had figured they had been up all night again trying to find their special talents

"You've been up all night again haven't you?" she said looking at the other two fillies.

"No miss we…"

*RRIIIIIIINNNNNNNGGGGGG*

Before Sweetie Belle could explain the end of school bell rang and the students prepared to leave

"You three stay behind, I'll have to talk to your Guardians" prevented from leaving the three Cutie Mark Crusaders sat there looking at each other.

**30 Minutes Later**

Now fed up waiting for Sweetie Belle, The Doctor entered the school to find out where she was. Ignoring the reception The Doctor began looking through every class room door searching for the little filly, finally reaching a class with three fillies and a pink mare

*Knock Knock*

"Come in" Cheerilee said hearing somepony knocking on her class room door

"hello, I'm Time Keeper, I'm here to collect Sweetie Belle" after The Doctors visit to the future he adopted a name most of the soldiers called him, since being his actual name would confuse everypony and it would keep his existence a secret

"ahh, I sent a message to Rarity, you must be her coltfriend" instantly The Doctor began to blush and Sweetie Belle felt confused since Rarity had never mentioned him

"oh no no, I'm just a friend, she just asked me to take care of Sweetie Belle for a week, her being on a business trip" Sweetie Belle looked over Time Keeper unable to remember where she had seen him

"Well in that case, I need to talk to you about Sweetie Belles well being" The Doctor looked over to the fillies with a look of confusion and back to their teacher

"I don't suppose it's that bad; can it not wait till Rarity gets back?" The Doctor asked trying to get out of this discussion

"I'm afraid not, I'm just concerned about Sweetie belle and her friends, they stay up all night and it's disrupting their learning" Cheerilee explained with a serious yet caring tone

"Yes…of course, that is important…I'll talk to Rarity and…" The Doctor was still trying to avoid the subject and attempted to get the kids out and gone, walking over and pushing sweetie Belle AND Apple Bloom out "and Apple Jack about this… as well as whoever takes care of this orange one" The Doctor continued signalling Scootaloo to follow

"But Mr Keeper I must…" Cheerilee tried to stop The Doctor in order to speak to him but as quick as he came in he was up and gone "what a strange stallion…why does Rarity date these guys?"

Outside The Doctor was walking away from the school with the three fillies in tow, heading towards a large blue box standing on a street corner

"Thanks mister, you really saved our skins" Apple Bloom thanked

"Anytime Apple Bloom, anyway I might as well drop you off to your place since I have the chance" The Doctor said before turning to face Scootaloo "what about you where do you live?" it was a bit awkward that a stallion she had never met asking her where she lived, that and she never told anybody she always directed her friends to her tree house

"Umm, it's okay I can walk back" Scootaloo attempted to get away but as she took a couple of steps the crashing sound of thunder rang through the sky as the weather team shifted the clouds for a storm

"Oh yea, I forgot a storm was scheduled for this afternoon. Ok then no excuses get in the box kids!" his instructions were a bit odd to say the least but as The Doctor gave a whistle the doors of the wooden box opened allowing light to be poured out, the three girls looked at each other and entered the strange box as the heavy rain began to fall followed by The Doctor closing the door behind him

**Tardis Control Room**

"What in the hay!" Apple bloom exclaimed as she took in the vast interior of the stranger's box, the dome shaped walls were made of metal with six metal support structures keeping the roof up and several lights evenly scattered around giving the room light, in the centre was a hexagon shaped console with a glass hexagon prism glowing a bright green connecting the console to the ceiling, at the edge of the large room was two doors leading out and a stair case leading below the cold metal floor

"it must me some kind of enlargement magic, you know making the inside bigger to fit more things" Sweetie Belle followed trying to explain how the interior could fit

"And how do you know that, he could be an alien and this might be his space ship and the outside is just camouflage" The Doctor paused for a moment and replayed Scootaloo's idea in his head, he was surprised both Luna and Twilight claimed the inside to be magic but this little filly had **'guessed' **the basic idea of his home.

"_well well, smart girl_" he thought to himself "anyway, welcome kids to my home"

"what is this place?" Sweetie belle asked staring at the dome-like structure.

"it's called the Tardis, a time machine that can go anywhere in the universe" The Doctor explained before the three fillies eyes widened in excitement.

"WHOA!" then in a split second the girls zoomed past The Doctor and began pressing buttons on the console.

"HEY! Stop that" The Doctor shouted trying to stop the trio from ruining his ship.

"What does this do?" Apple Bloom asked about to press a blinking blue button.

"That's the internal stabilizers AND DON'T TOUCH" The Doctor replied before grabbing Apple bloom just as she pressed the button.

"I'm a time traveller! Doing time travelling stuff" The Doctor turned to see Sweetie Belle jumping on the console pressing the temporal controls and as the Doctor went to get her off, he failed to notice the monitor displaying a destination date.

"DO NOT JUMP ON MY TARDIS!, she is not a toy, she is the most advanced piece of technology in the multiverse..." After telling Apple Bloom and Sweetie Belle off, he realised he missed something or someone "where is..."

"Hey what does this thing do?" Snapping his head towards the console The Doctors eyes filled with fear as Scootaloo was holding the Time Rotor hand brake.

"Don't touch...!" but it was too late, immediately after releasing the brake the Tardis began to take off but as The Doctor went for the fast return, he fell flat on his face due to the turbulence from the deactivation of the stabilizers, it also became apartment that the Tardis was dangerously low on power as a large bell began to ring from afar (somehow) and the lights began flashing red.

"What's happenin?!" Apple Bloom exclaimed while struggling to stand up right.

"Give me a Sec" The Doctor had gotten up and made his way to the console and started working at the controls using his wings to handle the smaller ones and as soon as he slammed the button next to the lever Scootaloo pulled, the lever snapped back in place and the Tardis halted followed by the sound of the power failing "NO!, no no no, why! Don't do this to me old girl" The Doctor attempted to keep his ship alive but was unable to save her as the lights dimmed with loss of power. When the fillies regained their balance they all stood silently as looked at the Pegasus with his head down.

"Mr Keeper, are you ok?" Sweetie Belle asked before the Time Lord lifted his head and looked behind him at the three fillies.

"Yea, I'm fine" The Doctor left the console and sat on the sofa at the edge of the room.

"I think we better go" Apple bloom said as she turned towards the door only to be stopped by The Doctor

"I wouldn't, we have no idea where we are. Soon as you step outside anything could happen, shot, suffocate, freeze, boil or even worse Rarity's Room, no that was a surprise landing"

"What do you mean you don't know where we are? We are just outside the school" Scootaloo said unknowing of what she had actually done

"Correction, we _were _just outside the school but all you're jumping around and pressing every button you could see, was the equivalent to setting the controls to random. The Tardis had left were it was and has moved somewhere completely different" The Doctor explained calmly as the three fillies looked down in shame, they were kind of used to being told off but The Doctor didn't get angry nor yell at them

"But you have wings can't you fly to ponyville and get help?" Sweetie Belle asked

"Sorry kid but the Tardis travels though time as well as space so I can't fly to somewhere if it's in the future or past plus if we are on a different planet, can't breathe in space so…"

"What is actually wrong with this thing anyway?" Scootaloo asked rather bluntly

"The ship was refuelling when you came in, It could move around Equestria perfectly well on backup power but jumping time zones is where the energy is really needed and we just didn't have enough, we will be fine though in a couple months the Tardis should have enough energy for a one way trip back however, I can risk leaving without knowing at least external readings…" The Doctor took a second to think before looking at Sweetie Bell more specifically her horn "AHA! I have an idea, Sweetie Belle how much magic can you charge up?" Sweetie's eyes widened in surprise at The Doctors sudden out burst

"Not much, I'm not very skilled at magic like my sis or Twilight" The Doctor then ran down the set of stairs leading down while shouting back up

"oh don't put yourself down like that, no one can out do Twilight" at first The Doctor's advice seemed helpful but his idea of helpful was very different "I mean come on the girls talent is magic for crying out loud" The Doctor flew back up carrying a fairly large machine, noticing that his word hadn't helped "your sister on the other hand, she is just a fashion designer but you little girl have the potential to outshine anyone…" with an epic save from The Doctor, Sweetie Belle eyes shined with determination "any way, all I need is a spark" he said before placing a metal cone on Sweetie Belle's horn

"Well here goes nothing" as she began to try and create a spark The Doctor hooked the machine into a slot on the console and the connection started up the machine

"What is that?" Apple Bloom asked

"It's a Magical energy transformer" he explained while checking the readings on the machine

"What does it turn into?" Scootaloo followed since Ponies had never really needed transformers so it made sense how she wouldn't know anything about it

"Oh, sorry it doesn't, it transforms other things, it can turn magical energy into Electrical energy which is what I need to power the console" The Doctor said while writing on a white board as a diagram

"Will that get us home?" Apple Bloom asked with hope in her eyes

"Nope we need artron energy to get home but the Tardis can recharge on electrical energy if she has some to work with" as The Doctor explained what they needed to get home, Sweetie Belle went from a tense state and immediately relaxed taking a breath prompting The Doctor to again check the readings

"Nope not even a watt" The Doctor said before looking at the small unicorns

"I'm sorry Mr Keeper, I told you I was never any good at magic" then The Doctor chuckled

"Well you're not going to get anywhere with tensing up all the time, if you relax while concentrating it will come naturally to you, same principle for all magic techniques" The Doctor said while getting up

"How would you know that you're a Pegasus" The Doctor looked at Scootaloo with a stern look then immediately back to a cheerful state

"Time Lord and I've read every of books by Starswirl the Bearded, if I was a unicorn I would surpass him easily…" as he went below levels the girls all gathered

"I'm sorry guys I don't think I can do it" Sweetie Belle said looking down at her failure

"It's not your fault Sweetie Belle, just take his advice and relax" Scootaloo added to cheer her up

"Yea don't force it, unless you know use the Force" Apple Bloom said referencing her favourite book by T.K Lord, Star Wars

"oh, you've read it two, I heard the author was writing prequels" as Scootaloo and Apple Bloom spoke about the book, Sweetie Belle remembered what the book said about the Force, she imagined a spark in her mind and after a few seconds the gauge on the transformer began to rise just a bit, she was about to do it but her concentration was broken by a certain loud mouthed Pegasus or rather both of them

"NO WAY! Ben Kenobi would have totally beat up Vader if he didn't give up" Scootaloo shouted in order to win an argument over Apple Bloom, Sweetie belle was about resume but again was interrupted

"GUY! No worries, found battery to power the console" The Doctor shouted at he flew over the console and connected the plastic block known as a battery to the console and with a spark, monitor activated followed by Sweetie Bell throwing the conductor on her head to the floor in rage but had quickly overcome her anger "right, just need to calibrate the scanners and we will be able to see what's outside" after adjusting a couple of dials the screen began to static and an image formed on it, it looked a normal street except that something was making the Tardis see itself like the houses were mirrors

"Why can we see the box?" Scootaloo asked looking to the large equine for answers

"I don't know, it's your universe not mine. Hold on let me get a technical reading on the environment" again pressing a few buttons the image resized and moved itself to the corner while the rest of the screen began showing a bunch of oddly drawn circles, as The Fillies stared at them unable to understand them, The Doctors eyes looked at the screen as if he was reading Equestrian "well well, this is interesting

"What is it Mr Keeper?" Sweetie Belle asked on behalf of the trio

"Well, the good news is that we are on Gaia so we haven't left the planet, the interesting news is that we appear to be on a crystal surface…and stop calling be Mr Keeper, it was annoying enough with your teacher calling me that"

"What's the bad news?" Scootaloo asked causing The Doctor and the other two girls to look at her "what!? Whenever someone mentions good news there is always a bad news"

"You've been reading Dash's Daring Do collection again haven't you?" Sweetie Belle asked knowing her orange friend

"Nope Star wars" then in an instant The Doctor, shot a look at the little Pegasus

"Ohh you guys have read it, I was wondering how people would like it" The Doctor said with Glee in his voice

"You've read it too!" Scootaloo replied with enthusiasm however The Doctor gave his usual smirk

"read it, please I wrote it" the little fillies eyes widened in shock and disbelief "T.K. Lord is me, T.K. for Time Keeper and Lord because I am a Time Lord, I'm not a fan of attracting attention" The Doctor looked at the currently expressionless face of Scootaloo and admitted a small detail "well I actually didn't right the story but the Lightsaber and Death star was my idea, I assure you. Anyway let's head out kids we got a crystal land to explore" as the three regained their senses they followed the grey Pegasus out the wooden doors.

**Unknown crystalline urban area**

Stepping outside the clear crystal architecture was in fact coloured, the house on the screen being a dark pink, with a purple roof and while the girls ran off to look at the beautifully built houses, The Doctor turned his head and spotted a cluster of pitch black crystals.

"This is amazing, wonder if we could ask'm to make are houses like this?" Apple Bloom spoke absolutely fascinated with the way the area was built, Scootaloo noticed That The Doctor wasn't next to him but nearly a yard away and on the other side of the street

"hey Keeper-guy, what are you doing?" she asked rather rudely

"My job and please call me Doctor" The Doctor replied taking out his sonic screwdriver and scanned the black crystal

"Doctor? Doctor of what?" The Doctor wasn't surprised nearly every being he met asked him the same question, a thing he inherited from his father after taking on the name, he then walked over and crouched to Scootaloo's eye level

"Does it matter, it's a name and that's all that should matter. I've learned that the name in this world tells a lot about the pony and it never occurred too many that it can also tell someone about themselves, your name is Scootaloo, it means something like mine is a promise I took in order to save it" The Doctor then returned to scanning the crystal with the now inspired Pegasus following him around

"By the way what is your job?" the orange Pegasus asked

"Royal protector of extraterrestrial and supernatural threats A.K.A Torchwood, my job is to keep Equestria and by extension the planet far from harm that could be caused by aliens and worldly dangers. So when you go to sleep Luna protects the kingdom but she doesn't do it alone far from it but the issue that I'm concerned with is this crystal isn't natural like it's synthetic" The Doctor then took out a thin metal stick and tapped the crystal only to be shocked forcing him to drop the stick "but it's loaded with magic, which is supposed to my natural" The Doctor then discreetly looked around while the other two fillies walked towards another black crystal

"Doctor are you ok?" Scootaloo asked noticing his ever growing concern

"Haven't you noticed? It's waaay too quite" listening in herself, Scootaloo heard nothing even Ponyville was never this quite at night and it was day time here, then just faintly she heard the sound of footsteps, as it got louder it was more clear that it was marching

"Doctor I hear people marching" his head snapping towards her as a reply The Doctor then saw the other two girls looking over another crystal that he was certain wasn't there when he left the Tardis, then again he noticed at the corner of his eye was another crystal grown almost instantly

"oh this can't be good" then black crystal quickly formed around The Doctors feet and the crystal in front of him began to glow in green and purple energy, then hearing the struggling cry's of Sweetie Belle and Apple Bloom, Scootaloo and the Doctor looked over to see them almost completely encased in crystal, the only person not affected was Scootaloo so on instinct The Doctor tried to save at least one "Scootaloo, quickly get back into the Tardis and wait in there till the power comes back on, no matter how long it takes" Scootaloo was now scared stepping back not knowing what to do, then following her footsteps was black crystal forming after she lifted her hoof

"What's happing Doc? What do I do?" The Doctor took out his screwdriver and a small grey plug.

"Do as I say, here" The Doctor said calmly before throwing the two items to the Pegasus filly "listen closely you're the only one free and I'm sorry but you have the least amount of consequences for aging quicker than other but listen plug that into the port next to the lever you pulled and once the power returns the Tardis will take you to Luna, give her my screwdriver and tell her what happened then take it from there, I'm sorry kid but I have no idea how long this could take but you can't leave the box under any circumstances, the Tardis will take care of you and don't worry no one will be able to get in, you'll be save" The Doctor was being covered more and more in crystal and was getting quicker as he spoke "please Scootaloo, you have to do this we haven't got a choice" and before being completely covered he gave a distinctive whistle and the Tardis doors swung open just as the marching was almost right on top of her, Quickly looking around she saw the crystalline forms of her best friends and The Doctor, frozen and helpless. a pony clad in black armour walked round a corner and shouted towards the frozen and Scootaloo who was backing into the Tardis Ever so slowly, as a mass of troops galloped towards the Tardis Scootaloo saw her friends begin to sink into the ground, now on her breaking point she leaped back once a troop has stood in front of her but hesitated once he saw the interior of the blue box. The Tardis taking the hesitance as a chance she shut her doors pushing the Troop across the street with incredible force.

**Tardis Control Room**

Scootaloo was cowering at the front entrance trying to make the pain go away but she kept saying in her head that it was her fault

"if I didn't pull that lever, none of this would be happening" Scootaloo was sobbing loudly and in the short time she had been in the Tardis she could tell no one else was here but that was never the case

"Don't cry Scootaloo" a sweet sounding female voice called out to Scootaloo causing her to look up covering her eyes from the light

"Who are you?" Scootaloo asked trying to see through the light

**Outside the Tardis'es present location**

As the last of The Doctor fell into the dark portal below the crystal attempted to cover the Tardis but it just covered an invisible shield around the blue box that none of the unicorns could counter.

The leader of the troops was overlooking the continued attempts to break into the box that one of the troops said was bigger on the inside and appearing the same way The Doctor and the fillies left was a black pony shaped shadow, the trooper captain turned but was unmoved by its presence but instead bowed before it

"My lord, three of the intruders have been captured but a fourth as taken refuge in the box however we are unable to penetrate its shields, it's magic is beyond any I've seen even yours my lord" the captain looked up to see sharp green eyes look down at him with a stern look making the captain tremble in fear "of course I am mistaken, not even Starswirl the Bearded could match you're unyielding power" the captain hoped that he would be spared at the hands of his master, as the shadow passed him it began to solidify and form a dark grey unicorn with a curved blood red tipped horn, his rear was covered in a red royal cape held in place by shining silver armour, his piercing green eyes looked upon the Tardis with a malicious smile on his face.

"You are forgiven captain. However this is no magic. The legendary box of ages…muhahaha, the time for my ultimate victory has finally arrived" then the captain turned to face his master only to feel a pulling force on his leg, he looked down to see that he was being dragged this death

"no! NO! Please my lord! I beg of you forgive me!" the unicorn turned his head to the falling captain with his malicious smile

"you have been forgiven, I just don't see the need to keep you alive" his final words to his loyal subordinate where followed by the final agonizing scream, the unicorn turned back to the box then turned back in to his shadow-like form speaking with a more demonic like voice _"SOON I EMPEROR SOMBRA SHALL BE THE MASTER OF TIME ITSELF! MUHAHAHAHA! HAHAHAHAHA!"_

TO BE CONTINUED

Next Time:

Escape from the Empire

Courier: ok guys I must confess, I used way to many Star Wars references and I couldn't help it but if I really was trapped in another universe that had never seen Star Wars I would novelise it

Plus it fits, the Crystal Empire on par with the galactic Empire, The characters connecting magic with the Force.

And I changed Sombra's title, I mean come on he is a tyrant over the Crystal EMPIRE and he calls himself a King, complete bull plus we have an evil queen, we have good princess so we know have an insane Emperor

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	14. Episode 13: Escape The Empire (Finale)

Courier: Finally the Season finale, who will win the epic battle between the Emperor of Shadow and the Lord of Time stay tuned to find out

Enjoy

Doctor Who:

The Equestrian Chronicles

Episode 13:

Escape from the Empire

**Crystal Palace Throne Room**

"What! Where am i? Where are the kids?" waking up from an uncomfortable nap, The Doctor searched the room for any sign of the fillies but instead felt a sharp pain in his side as a pony clad in black armour, Which looked oddly familiar, had jabbed The Doctor in his side "ahh! God dam it"

"So this is the legendary Pony of time, I am underwhelmed" Looking up, ignoring the pain sat a stallion with a similar coat to his own but instead was a unicorn with an oddly shaped horn, he also looked like he had a god complex judging by the royal cap and the Troopers.

"Oh don't worry, give it a minute and I assure you will be whelmed, now where are the kids!" The Doctor roared disregarding the fact that he was at this unicorn's mercy.

"Oh I would me more worried about you're self but if you must know, the children are in the dungeon and will await my decision about their fate" The Unicorn stated while teleporting towards The Doctor using the shadows.

"You have no idea who you're messing with do you?" The Doctor spoke with rage in his voice right in the unicorn's face yet keeping his composure.

"Oh, I know perfectly, I heard stories from my mentor and I read all the legends recorded throughout history and I must say you're such a disappointment"

"Is that so, do any of those stories mention what happens to idiots who threaten my friends and their families" the unicorn saw the look in the Time Lords eyes and it was more than enough to cause him to back away but he immediately stepped closer in hopes to cause him to fall back instead.

"How do I get past you're Time Machines shield?" still as a statue The Doctor looked dead into the Unicorns eyes.

"As long as I breathe you're not getting one extra second Sombra" the dark unicorn Emperor Sombra growled and walked back to his throne before snapping to the Pegasus "very well Time walker if you won't give me what I want then, you will lose what you strive to protect. The filly's deaths will be slow and entertaining" The Doctor gave a stern look but did not lose his temper, realising if he fought back know it would help Sombra more than it would help him.

"Fine kill them, you're still not getting my ship" he said looking away like he didn't care for the kids safety above control of time, Sombra on the other hand was furious when realised he would not win the Time Lord over.

"Take him back to his cell!" the troopers gave a few jabs to the Time Lord prompting him to move and The Doctor was then escorted out.

**Crystal palace spiral staircase**

While being escorted The Doctor had time to think as he had blacked out after being sealed in crystal. He had heard of Emperor Sombra vaguely from Luna after he asked about the Crystal Empire and had done some research and had learned enough to know he was bad news. According to the notes from Starswirl the Bearded, he was a brilliant student and was a master and verbal magic but was unable to cast regular spells due to his setback of being a Crystal pony and so by chance he had discovered Dark Magic, a magical art created and mastered by Cosmic Knight Guardian of the universe and King of Equestria before Celestia and Luna. However it was too dangerous for anyone but extremely powerful Alicorns, so the source of its knowledge, The Book of Shadows was locked away however its power fell into Sombra's hooves and using its power he changed his race to that of a unicorn, the consequences left him cruel, relentless and above all hungry for power. He had defeated everyone in his path ultimately Princess Luna defeated him but with things as they are The Doctor must get out of the Empire before Sombra is able to damage The continuum and ruin the future.

"So pleasant day we're having, you guys got anything planed for the weekend?" The Doctor was always good at bringing up conversations, usually to catch his enemies off guard while he escapes.

"Shut it, you are the prisoner of the emperor and you will obey him sooner or later" the trooper in front of him snapped.

"Why should I, I'm not even equestrian, Your Empire is just a foreign culture" The Doctor replied with a smile and to his luck the trooper behind him was light hearted.

"Is that so? so then where do you come from?" the back trooper asked out of curiosity, a trait both ponies and humanity shared.

"Don't encourage him, he's the enemy of the Emperor and has no rights in his Empire" the front trooper stopped and turned to shout at his obviously less intelligent partner.

"What? It was just a question" the light hearted trooper countered but the serious trooper was not having it.

"Don't you see, it's probably some trick in order to escape and it's our duty to make she he doesn't, is that understood!" the nicer trooper nodded his head in fear but were caught off guard by The Doctors sudden pop up.

"You know you really need to lighten up like you're friend here" The Doctor said to the angry trooper then turned to his imperial friend "the answer to your question is the planet Gallifrey and I have two things to say to you both"

"What!?" both troopers said one in annoyance and the other in curiosity.

"Rule 1, always cuff you're prisoners, and Rule 48, never let them stand next to a window" the thought had indeed occurred to both troopers that the Time Lord was in fact not bound and after taking a few steps back The Doctor fell through the window and down toward the ground several 100 feet below and as the guard looked down to see the demise of their escaped prisoner they instead witnessed The Pegasus open his large wings and soar to safety.

"Oh, we're so dead" the kind trooper said looking at the grey Pegasus soar away from the palace.

"YOU IDIOT! I told you, now after him" but as the angry trooper tried to walk away he was pulled back as he had been cuffed to his partner while they were arguing "F***! however I have to admit, the fool has style"

**Back at the Tardis'es location**

Now free The Doctor had to get the Tardis away from the Empire as quick as possible and free Sweetie Belle and Scootaloo from Sombra, he was surprised how there were no troopers guarding The Tardis. Unlike the many forms of attacks that attempted to penetrate The Tardis shield The Doctor landed and calmly walked through as if it wasn't even there.

"He he, if only those num nuts tried walking through unarmed" as The Doctor walked into his home he quickly scanned the room for Scootaloo but the filly was nowhere to be found "Scootaloo! It's The Doctor; you can come out…kid? Huh? She must me somewhere else…" The Doctor walked through the control room but froze when he saw what was on the Tardis monitor screen "oh no, Bloody hell! I told her but do they ever listen? _Noooo_" The Doctor went for his bag but saw it was missing "Dam it! That kid…THAT KID!…" The Doctors rage boiled for a few seconds before relaxing and had a massive smile on his face "reminds me of me when I was that age. HA!" running out of the Tardis doors the stopped and took out his key locking the box with a beep and the exterior vanishing like a mirage "try getting your greasy mits on my box know Sombrero" now having to find Scootaloo, The Doctor closed his eyes and listened "right you little scamp where are you?" and within a few second The Doctors eyes shot open and flashed white for a brief moment "got you" following Scootaloo's temporal trail The Doctor shot off and headed back toward the crystal palace.

**5 hour ago in the Tardis Control Room**

While Scootaloo was crying over the events that transpired, she failed to notice a golden glow around the Tardis console.

"Don't cry Scootaloo" a sweet sounding female voice called out to Scootaloo causing her to look up covering her eyes from the light.

"Who are you?" Scootaloo asked trying to see through the light, as it dimmed in front of her was a beautiful dark blue mare Alicorn with bright golden eyes and a mane similar to Princess Luna's, yet styled to look like the universe instead of the night, unlike the princess's however was that it didn't flow magically but instead fell down much like normal hair she was also the same size as Celestia and had a kind face with a cheerful glow.

"I am the type 45 Time Travel Capsule you are currently standing in" the mare said which made no sense to the filly.

"The what?" Scootaloo asked standing up.

"You also know me as Time and relative dimensions in space or Tardis, as I'm more commonly referred as" the mare claiming to be The Doctors home said.

"The Tardis?" Scootaloo looked around the room the back at the mare "isn't the Tardis a time machine?"

"I am but I do have a soul, a life and I am glad to have The Doctor as my friend and I would happily wait a long time to see him, a perk for having such a kind and sentimental owner" the supposed pony form of the Tardis walked towards the console and pointed at the monitor "I have been tasked to look after you but we have more important matters"

"Like what?" Scootaloo asked before looking at the monitor as it showed a dark unicorn with a curved red tipped horn "and who is that weirdo?"

"That is Emperor Sombra and he will try everything he has to break into me and have his way with me… that came out wrong, I need to rework my speech, I don't talk to people much" the Tardis cocked her head while thinking about her words before turning to Scootaloo "but there is something you must do"

"What?" the Tardis turned to a blue bag hanging on the coat rack "inside that bag is everything my owner needs, you must get it to him and tell him to signal the flare of attack"

"Why do we need a flare?" Scootaloo asked walking over to the bag.

"This date is close to the very day the crystal empire was lost and the princess must be called while Sombra is distracted by my owner and you are the only pony better yet living being I can verbally communicate with?" the Tardis spoke with a soft yet informative tone making Scootaloo's head swim with confusion.

"What the hay do you mean? I can barely understand you!" Scootaloo shouted at the demanding Tardis.

"And no one ever will. But we must get the future on the right track and to do that, the princess must be signalled to attack" as Scootaloo looked to the bag and back to the Tardis, she realised she had no choice but to trust her

"Ok, I'll do it. Where can I find The Doc?" Scootaloo asked grabbing the dark blue bag and slinging it over her.

"He will find you, you must go to the palace, rescue your friends and in the process find the red flare and fire it. Then after that all you have to do is escape" the Tardis looked to the door and it opened to the mass of troopers staring into the time machine "don't worry about them, juts run to the palace"

"But I can't fly, how do I get to the very top?" Scootaloo asked as she flapped her under developed wings.

"I don't know use the Force or something?" the Tardis said as she vanished before prompting Scootaloo to run.

"THERE! Get her!" the unicorn troopers lowed their horns to blast the filly but as Scootaloo looked in horror, all the guards vanished before being able to fire and after looking around the surroundings of the time machine she ran for the palace as quick as she could.

Back in the control room, the age old time lord entered worried for the orange filly s safety, but against his knowledge the monitor flickered to that of a blue print of the palace dungeons telling The Doctor exactly where he needed to go.

"Dam it! That kid…THAT KID!… Reminds me of me when I was that age. HA!"

**7 hours later, Crystal Palace dungeons**

Scootaloo walked through the dark dungeons, probably the only part of the palace that wasn't made of crystal, as she looked for her friends she didn't notice however a presence following her.

"Dam box pony! Made no sense what's so ever. I don't know who gave who what" as she peered round the corner, sitting behind her was a well-blended grey Pegasus.

"I don't know either any ideas?" jumping back several meter Scootaloo looked carefully to see The Doctor in the shadows.

"Doc! It's so good to see you" she yelled running up to The Doctor giving him a hug, something he did not return.

"Where have you been girl, I've been worried sick. Luckily I was able to escape but I had no idea where you had ran off too" it was then Scootaloo noticed something was off, the doctor had never called the girl before, he knew her name.

"Long story but come on we have to find my friends and get out of here" as she began to run ahead The Doctor didn't move causing Scootaloo to ask what was wrong "you ok Doc? Is something wrong?" the doctor looked down in sorrow but since he was still in the cover of darkness Scootaloo didn't notice the sinister smirk he possessed.

"I'm sorry child; your friends are already dead. I tried to save them but they were executed before I could get to them" as Scootaloo denied her friends demise she collapsed and began to cry once again but she still had a job to do "come child we must return to the time machine" as The Doctor turned to leave, Scootaloo's eyes shot open when he heard The Doctor speak of the Tardis.

"What was that? Doctor!" the time lord turned to the filly with an impatient expression.

"Did you not here me! We are going back to the time machine; if I can't save your friends then at least I can save you" however before Scootaloo could react, she heard a familiar voice coming from the other end of the hallway.

"Well you did a terrible job at saving, had to waste an hour looking for these two, then another looking for the orange one" standing proudly and with a cheeky smirk on his face, stood another pony who looked exactly like The Doctor but Scootaloo could see the difference, that stallion was The Doctor proof in the matter as he was pulling a trolley with two unconscious fillies on top.

"I have a name you know!?" Scootaloo yelled in annoyance.

"But you are orange, I wouldn't care if you called me the grey one but then I sound like an old wizard" The Doctor continued as he walked up to Scootaloo ruffling her hair then staring into his doppelgangers eyes "you're not fooling anyone Sombra take that ugly disguise off it doesn't suit you, I mean who would want to look like that"

"Uhh, Doc he's trying to impersonate you" Scootaloo mentioned prompting The Doctor to look down and back to the disguised Sombra who had adopted a maniacal grin.

"Oh right, I forgot I looked like that. It's been a while since I looked in the mirror" as The Doctor pondered over his appearance, Sombra shifted back to his original form.

"Who needs to fool, you are the key to getting into your time machine and you came back for those petty foals" Sombra said before giving a small laugh which prompted Scootaloo to step back in fear but as she looked up to the Time Lord he was unphased, in fact he had lost his cheerful face and Scootaloo could finally see his age.

"Like I told you, you're not getting one second of extra time" The Doctor then turned his head to face Scootaloo "kid get your friends out of here, I'll meet you back at the Tardis"

"No!" Scootaloo shouted in refusal.

"Scootaloo! Do as I say!" The Doctor barked, the serious tone in his voice had frightened Scootaloo but she kept her cool and did what the Tardis had told her to do but not before shedding a tear.

"Not before you take this" Scootaloo shot back handing The Doctor the blue bag "also we need to signal the princess's to attack!"

"Who told you that?" The Doctor asked calming down slowly but not taking his eyes of his opponent.

"Doesn't matter right now! Just trust me on this Doc. Ok" The Doctor looked at the young filly's face and it was just then he saw the tears. Had he made her cry?

"Ok. I trust you, now go head to the Tardis. And stay there this time!" The Doctor ordered gently with the small filly nodding in agreement before leaving with her friends still unconscious. Sombra after waiting patiently for his battle drew a scythe from the shadows and The Doctor walked over to his bag and pulled out his screwdriver and black Katana, after holstering his screwdriver, The Doctor faced Sombra holding the grip of the sword and the sheath with each wing "Emperor Sombra as an agent of her majesty Princess Celestia's royal Guard. I hereby order your complete and total surrender" though he was serious in his demand Sombra burst out laughing.

"Muhahaha! You Think I'll surrender Time walker! Never" Sombra raised his scythe ready to attack while The Doctor drew his sword only ever so slightly.

"That's Time 'LORD' and I'm trying a new approach to dealing with my opponents" pulling the rest of his sword out he tossed the sheath and held the blade in front of him eyes resting on the tyrant "Avanti" using it as a signal both stallions shot towards one another unsure of who cut who.

**Back at the Tardis**

As Scootaloo ran as fast as she could with the weight of her friends behind her she eventually reached the blue box, however before opening the door Scootaloo noticed a small box by the door. Opening it she saw a strange device that was obviously not operated by ponies, it had a curved handle and a tiny pull lever with a barrel at the front, beside it was two cylinders and a piece of paper. Picking up the note it read.

_Scootaloo_

_I wasn't able to get a shot off with this, so I'm leaving the job to you and your friends, fire the purple one first followed by the blue_

_Good Luck_

_Doctor_

After reading the note carefully Scootaloo heard Sweetie Belle waking up.

"Uhh, My head, last thing i remember..." as her memories returned she shot up and looked around for her friends, she spotted Apple Bloom beside her unconscious and was relived to see Scootaloo walking up to her "Scootaloo! Are you ok?"

"I'm fine Sweetie Belle But i need your help"

**Crystal Palace throne room**

The fight between The Doctor and Sombra had intensified with The Doctor bursting through the floor of the throne room and crashing into the ceiling before falling hard onto the ground; Sombra had slithered through the hole in the floor in his shadow form and solidified walking slowly towards the Time Lord.

"I'm disappointed, my mentor spoke of you highly, he spoke of legends of the keeper of time and his many bouts with gods and demons; and here i thought you'd be more of a challenge" The Doctor struggled to get up but ignored the pain pointing his blade at the Emperor.

"I'm not here to fight you. I have a duty to protect those kids and if changing history is what it takes then so be it" as The Doctors rage began to build Sombra hesitated when he saw a glow cover him like a vial much like the Darkness does him, taking a stance to prepare for The Doctors strike he was surprised when The Doctor had vanished and in the same second felt a sharp intense pain; he had been stabbed by The Doctor from behind.

"How did!?" Sombra questioned before coughing up a fair bit of blood.

"I move so quickly? I've studied almost the entire history of magic and every spell from now to the next millennia and i've learned to channel flight magic into pure speed. The stories you've been told are of my future and if I've really fought with the gods and demons of your past...that's i guy i don't wouldn't want to have a grudge against you" Sombra using his Shadow magic teleported to the opposite end of the room and healed his wounds _**"bugger, if this guy can heal from that, I have no idea what can disable him let alone kill him, come on Scoot i need back up"**_

**Royal Army HQ west of the Crystal Empire**

Celestia never did like war; it always brought out the worst in her. This was the 4th war she was in and she was just glad her kingdom wasn't in danger.

"You're highness Princess Luna has arrived" the captain of the Royal guard announced bringing the Princess out of her trance as she looked on to the Empire she had left in her best friends care.

"Thank you captain" as she got up to greet her sister she couldn't help but remember the very day she was told Sombra had declared himself Emperor.

**The Tardis landing site**

"So you want me to use my magic to fire that in the sky to signal the princess"

"Pretty much" Scootaloo confirmed as Sweetie Belle played through the plan in her head.

"Well I would love to help but i can't use magic that well yet"

"Come on Sweetie Belle could you at least try?" Scootaloo's encouragement reminded Sweetie Belle of the moment in the Tardis and she figured that she had a shot.

"OK I'll give it a go" walking across to the odd device Sweetie Belle began to concentrate but this time going back on The Doctors advice.

"_If you relax while concentrating it will come naturally to you, same principle for all magic techniques" _as she concentrated she pictured the flare gun and imagined it lifting up after a few seconds, he concentration was broken by Scootaloo.

"Whoa" she said in astonishment, distracting the young unicorn.

"Scootaloo I need to concentrate!" Scootaloo pointed the other way in response and when Sweetie Belle turned she saw the device floating in a clear aura, it took her a second to process that it was her that was lifting it "i did it" happy that she had used a successful levitation spell she turned to Scootaloo who was smiling in amazement and overjoyed for her friend.

"Nice job Sweetie Belle, now it's time to call in the troops" now confident she could help, Sweetie Belle agreed and pictured the small cylinder with the red markings going in flare gun and so her magic reacted and picked up the cylinder and inserted it into the device.

"Here goes nothing" pointing the gun upwards she focused on the trigger and with a thought the gun fired and a small cloud of red smoke was spread out across the sky.

"Now for the other one" Scootaloo said before Sweetie Belle loaded the flare gun with the blue cylinder.

**Outside the Royal Army HQ**

Celestia stepped outside fitted in golden armour and her hair flowing in the Arctic wind, just landing was Luna wearing a dark cloak with her hair tied in a ponytail.

"Luna glad to have you here, how is the kingdom?" Celestia greeted putting any current issues aside.

"Well sister, though the peasants are getting restless, i hope this war will end soon" Luna replied before looking on to the Empire "i do not know why we haven't assaulted Sombra yet, his army it pitiful compared to the royal knights"

"Maybe so but Sombra is extremely powerful and dangerous in his own right, we will attack as soon as the strike team signal us; now i suggest some tea to calm the nerves" as Celestia walked back to her tent, Luna called for her attention when she turned her eyes way from the Empire.

"Celestia Look!" turning back she saw a cloud of red smoke, signalling that the Empire was to be attacked "shall I ready the soldiers?" before Celestia could give the order she noticed another cloud, a blue one. Gazing upon the second cloud her heart froze as it could only mean one thing "Sister?"

"Luna ready your armour and order the troops to stand down" this response confused Luna, it was Celestia's idea to set up an elite platoon for this very moment and she was not going to use it.

"What? Why you said that you were waiting for the signal and there it is, why do you order your elite not to fight?" Celestia continued to stare at the blue coloured cloud and for once in a very long time, spoke with a very serious look in her eye.

"Because we do not need them" Luna looked back to the Empire and to the blue cloud.

"_It's that second signal…Blue? there isn't a blue flare, is there?"_ trusting her sisters words Luna left to suit up.

"What have you gotten yourself into this time old friend" Celestia said to herself before leaving to gather he helmet and spear.

**Crystal Palace throne room**

The Doctor and Sombra fought for what seemed like hours but with The Doctors Speed and Sombra's ability to heal the battle were going nowhere but The Doctor was already bleeding and he would give out sooner or later.

"Come on then Sombra is this the best you got, my grandma has more power in her slap and she's over four thousand" The Doctor joked ignoring his injuries but Sombra simply laughed "what's so funny"

"You bore me with your humours comments. You can't fool me, fear is my speciality. You laugh and joke throughout time to ease the pain and forget the darkness, The Jester, The Trickster, The Mad Man, some of the names that tales of legend refer to you as but there are other more accurate ones, The Myth, The Descending Rage, The Destroyer of worlds, come Time 'Lord' so me your rage, give in to the Darkness" The Doctor paused, he would be called those things, either mocked at or feared, all the work to protect the innocent and that's how they see him. "Maybe if I kill those children" then he snapped The Doctor rushed forward in pure anger.

"LEAVE THEM OUT OF THIS!" the shear speed The Doctor flew at shattered every window and in that split second Sombra covered the Time Lord in a veil of darkness halting his assault and after passing through crashed hard on the floor.

"There it is, the rage I heard of, now witness you true fear" satisfied with the battles turnout Sombra turned to leave noticing the red and blue flares as they were dissipating. The Doctor however got up in pain, breathing heavily his eyes turned dark green. He was in a state of pure panic, in the walls of his mind The Doctor saw the one thing he never wanted to see and he knew it would break him.

"You think fear can stop me?" The Doctor said quietly yet with his foe still able to hear.

"Hmm?" Sombra turned to face his foe who as he turned around himself had tears in his eyes.

"My greatest fear...being forgotten, sure I may be laughed at and some of my tale s will frighten children and adults alike but that one thing that lingers in the back of my mind, the one thing I fear…is the one thing that keeps me fighting" then The Doctors tear filled face changed the expression of sheer rage and unlike his previous outburst there was no deafening roar of anger, no bone shattering strike just the look of pure unrelenting rage "and no matter what you say or do. I will never be alone" then as both stared each other down Sombra had noticed that The Doctor had reacquired his sword and the rubble from the destruction caused during the battle began to rise from the ground around his opponent.

"What is happening!?" Sombra demanded and without any explanation, The Doctor took a pose holding his blade in a position ready to swing. Sombra no taking any chances shot for the Time Lord in hopes of dealing the final blow however The Doctor, calm and collected and filled with 300 year old anger, closed and breathed in deeply and with his heightened perception listened as Time began to crawl, he sensed Sombra soar through the air weapon in hand half way across the room and prediction the right moment The Doctor opened his eyes his dark brown eyes replaced with pure light and in that very moment swung his sword.

"Checkmate" Sombra had stopped dead in his tracks yet he was still in mid-air suspended, as a few seconds had passed a Sombra's features began to dull and grey and the Dark Emperor turned to stone followed by time returning to normal speed allowing the now stone form of Sombra fall to the ground, the force of which shattered the tyrant into dust, his shadow slithering away was his body crumbled. As The Doctor took a sigh of relief he began to fall however when he lost consciousness he was caught by a slender figure clad in black armour.

**Sometime later**

As The Doctor came to the first thing he saw was Scootaloo trying to get him up.

"Doc! Come on Doc wake up!" a small smile grew across The Doctors face as he relaxed after a hard day of work.

"Nah, five more minutes" he said ready to fall asleep but the sound of a very familiar voice caught his attention.

"You seriously are going to joke after your ordeal" upon hearing said voice The Doctor stood up in an instant.

"LUNA! How did you get here!" the Time Lord said on instinct thinking this Luna to be the present Luna.

"Me and my sister where signalled here but when we arrived you had already taken care of the tyrant" the princess said coldly and almost disappointed.

"Oh, so I guess it was you who got me out then?" The Doctor asked noticing he was outside.

"Indeed my sister asked me to bring you to this box and allow you to leave…" The Doctor nodded before turning to see Scootaloo, who was smiling at the fact The Doctor was okay along with Sweetie Belle, who was tending to Apple Bloom, who was still unconscious, then the Time Lord turned back to the princess.

"Well then Luna, thank you but Celestia is right I must be off, come on kids we gotta go" the Doctor said before realising he didn't have his bag.

"Looking for this?" Luna asked followed by The Doctor turning to see Luna holding up his bag and sword with her magic.

"Yes thank you" as he went to grab his equipment she moved them out of his reach.

"But first I want you to tell me who you are?" The Doctor stood still hesitating before he answered.

"I'm afraid I can't tell you but I can say we are very close in the future but that is something you will have to wait for" Luna felt unsatisfied but if Celestia trusted him she would just have to accept it.

"Very well but the next time we meet you are going to tell me everything" the princess demanded handing the Time Lord his things.

"Good thing I already did" The Doctor said with a smile before Luna shot off into the sky "dam she was a cold character in the past" turning to attend to the kids Apple Bloom slowly woke up.

"Uhh…hey guys" looking around the young earth pony saw both her friends happy that she was ok and The Doctor who was covered with bruises and cuts "Did I miss anything?" she asked unable to remember why she was unconscious in the first place.

"We'll tell you inside Apple Bloom" nodding in agreement all three fillies walked into the Tardis but as The Doctor entered he looked back at the legendary Empire "I'll be back"

Next Time:

The End

Courier: now I was planning to do something with Scootaloo but I was already three quarters though the episode when I thought of it so I'm going to build that in the shorts and future episodes but I will be key for future plots.

By the way this is the last episode of Season 1 and the next episode I will try to release by Christmas Day.

So what did you think of Season one. It is open to be rewritten but I would like some major feedback from you all so right a review about what you liked and didn't, things you'd change of others you could see improved.

Thank you all for reading and hope for a great Doctor who Xmas Special and return of MLP: FIM season 5.

Till then guys keep reading

Avanti!

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


	15. Xmas Special: The End

Courier: **In Memory of fellow fanfic writer and Brony, Adam Smith 19**

**Committed suicide as a result of cyber bulling.**

**I didn't write this for him but every single word I type from now on will be for people like Adam**

**And I will never give up **

Enjoy

Doctor Who:

The Equestrian Chronicles

The End

**Ponyville**

Morning was settling in Ponyville but due to the winter cold, many stayed in the warm while children ran out to play in the snow. Outside sugar cube corner Mrs Cake was disposing of the out of date stock when she was startled by someone behind her.

"Oh my dear, you scared me there…" the pony behind her was extremely skinny with bits of his flesh were missing from his body but it wasn't noticeable as he stood in the shadows, his head was tilted slightly like a curious animal "are you okay"

"My Time is running out" his voice was young but drowned out by another much deeper voice "but Time cannot be earned, it cannot be found"

"Excuse me?" Mrs Cake said while the stallion's eyes began to glow bright red.

"But it can be taken" it was then the Stallion's head cracked straight and his jaw unhinged, a bright blue energy began to flow into his mouth from Mrs cake who felt very different and upon inspection of her hooves saw her skin shrivel and her vision began to cloud and a terrified scream could be heard all across Ponyville. As the blue energy stopped the Stallion's body began to click and snap with the missing parts beginning to rejuvenate "you had much time but none to spare, I must find the Timeless one but I require extra time to gain more time"

**At the same moment**

Across town both Twilight and The Doctor where going out for something to eat to celebrate the festive season.

"I swear this restaurant is Amazing, I have never tasted better soup" The Doctor exclaimed.

"Well at least you're not eating meat, since you're not Equestrian I don't mind but really, eating animals is just wrong" Twilight replied disapproving of the meat The Doctor eats on a daily basis.

"But it's good for you, Meat is full of proteins and meaty goodness" The Doctor wailed like a child before being attracted to the ear piercing sound of a mares scream "what was that!?" immediately Twilight ran towards the source of the scream with The Doctor right behind her.

"That wasn't too far from sugar cube corner" Twilight informed her friend as both cut threw alleyways to get to their new destination.

**Sugar Cube Corner**

As the Two friends came within vicinity of the bakery both saw both Mr Cake and Pinkie Pie also inspecting the scream with Mr Cake calling for his wife.

"Twilight!" Pinkie shouted signalling her to come over.

"Pinkie what happened?" Twilight asked as The Doctor whipped out his sonic screwdriver and scanned the area.

"We heard Mrs Cake scream but when we came out, she was gone" Twilight suspected kidnapping but it made little sense but before she could ponder the thought she was called over by The Doctor who was pointing his screwdriver at the floor.

"What is it Doctor?" Twilight asked with pinkie listening in but The Doctor turned his attention to Mr Cake and flashed his psychic paper.

"Excuse me sir, I'm with the royal investigation bureau, I understand your wife is missing" The Doctor shot down Mr Cakes attempts to discuss the matter while he tried to explain to the poor soul "so I ask that you go and look for her, she couldn't have gotten far considering" Mr Cake then frowned at the Time Lord for his comment.

"What are you implying Sir!" he said angrily making the situation very awkward for The Doctor.

"Well…uh, if she was kidnapped it would be pretty difficult to carry a full grown mare without being seen. Please sir I'm a professional, just listen to me and go find your wife. I will investigate her last known location for evidence in the meantime…" prompting Mr Cake to go with a 'shoo' motion, the man in question left the area in search of his dear wife.

"I should go too, I mean we need to get a search party going" Pinkie offered in a surprisingly mature way.

"No point, he isn't going to find her" The Doctor said in response making both pink and purple mares frown.

"Doctor that's not a very nice thing to say" Twilight said making sure Pinkie would pounce for The Doctor.

"Whoa hold it, I only told him to do that so I could get to work and actually find Mrs Cake or would you like me to involve the entire town" The Doctor explained himself primarily to Pinkie, he then proceeded back to the position he was earlier and took out a compass.

"You better find her!" Pinkie growled while the Time Lord began to work.

"So what was it you wanted to talk about?" Twilight asked as The Doctor flipped his compass yet the compass continued to spin "and why do you have a broken compass?"

"It's not broken, its enchanted, a gift from an old pirate friend of mine, it doesn't point north but instead it points you to the thing you want most, so…" it was then that The Doctor threw the compass to Pinkie.

"What am I supposed to do with this?" Pinkie asked opening the compass.

"To be honest it would work better with Mr Cake but I can't involve him. I have a hunch…so Pinkie what is the thing you want most right now?" The Doctor asked the party pony as she raised an eyebrow.

"To find Mrs Cake…Doc I may be all for a good joke but this is a serious matter" but when she revealed her goal the north arrow pointed towards the bin and The Doctor zoomed to Pinkie Pie to see, he the snatched the compass out of her hooves and put it back in his bag taking out his screwdriver once more scanning the not the bin but a small pile of ash in front of the bin.

"Doctor! Stop with the Sherlock hooves routine and just tell us what are you doing?" Twilight shouted frustrated with the way The Doctor was acting. In response The Doctor deactivated his screwdriver and bowed his head in sorrow.

"I had a hunch…when we arrived I felt a temporal disturbance, plus this ash pile in front of the bins. Pinkie what was Mrs Cake doing?" The Doctor asked a now relatively calm Pinkie.

"Taking out the stale stock" she answered with a confused tone.

"Well then, Mrs Cake isn't missing…this ash pile is brimming with DNA, Pony DNA" Twilight gasped as she connected the dots while Pinkie was struggling to understand.

"What are you saying Doctor?" The Doctor didn't bother to answer and attempted to avoid the subject.

"Pinkie go and get Mr Cake tell him that we have a lead and are doing the best we can to get his wife back" Pinkie was going to turn and leave but she needed to know if she was telling the truth.

"Will you?" she asked The Doctor who looked coldly in her eyes.

"Go Pinkie. Please" obeying her friends instruction Pinkie left to go find Mr Cake, Twilight however was still shocked "why can't I have just one holiday without some disaster happening"

"Is she...?" Twilight began to ask but it was a little too much for her to sink in.

"Yea, Mrs Cake is dead" confirming her suspicions Twilight collapsed.

"Do…do you know how?" The Doctor looked to his best friend then took out a small vacuum and hovered the ash up.

"Sorry Mrs Cake but your remains are evidence. I'll now more when I analyse the…um body" The Doctor explained helping Twilight up and both headed For the Tardis.

**Tardis Laboratory**

It had taken three months for The Doctor to show Twilight the Tardis, mostly because the crusaders began to brag and Twilight got a little jealous. Twilight spent a good week in the Tardis but her favourite room was at the moment the Lab, since the Library was still being manually refurbished. The Doctor had begun analysing the dusty remains of Mrs Cake while Twilight plugged the Sonic Screwdriver into the computer to inspect the scans.

"Now that is interesting" The Doctor quietly said to himself just as the results from the scans came back.

"Doctor it seems there was an enhanced Temporal ripple directly where the ash pile was and it seems to have flowed out, like something was being drained" The Doctor came over to look at the scans and was definitely intrigued.

"How very interesting…" The Doctor pondered the thoughts swimming in his head and would have stayed silent but that was probably why he enjoyed a friend to help out. to have someone to talk to "I found that the ash wasn't burnt by fire"

"It isn't ash, so what is it?" Twilight commented but The Doctor shook his head in disagreement.

"No its still ash but it was burnt by time" Twilight raised an eyebrow but could understand that The Doctor had an explanation to this "you see when something ages, it will eventually degrades into dust and by then it would be buried in the soil but if you force something to age it burns and turns into ash, so Mrs wasn't disintegrated but forced to age at an alarming rate…ouch"

"Why ouch?" twilight asked still trying to grasp the Method of Mrs Cakes death.

"Ok, I can put it in to ways, one her cells where forced to decay at a much faster rate but this isn't likely as it would have left an actual body, Two every ounce of artron energy was drained from her body. This is the mostly likely as this can cause temporal burn and it would explain the scan data" The Doctor walked over to the black board on his wall and began making calculations.

"What's artron energy?" The Doctor looked back at his friend and quickly explained.

"Temporal energy, it's one of the things necessary for time travel and therefore exists everywhere, it's what the Tardis was fuelled by in my universe but Magic is a much larger source hence the incident several months back" getting back to his calculations the phone next to the door began to ring "really, what could be so important that I need to be interrupted now!" Picking up the phone The Doctor didn't have a chance to greet as on the other end was an extremely worried Luna.

"Doctor get over here now!" as soon as Luna finished her message The Doctor ran for the control room and set the controls for canterlot.

**Canterlot Palace Throne Room**

Literately seconds after hanging up the phone The Doctor burst through the doors.

"Doctor!" Luna shouted with enthusiasm upon his arrival, luckily Luna was in no direct danger.

"Luna! Thank Rassilon you're ok" The Doctor also yelled hugging Luna in relief making Twilight and several of the guards smile, when The Doctor realised what he was doing he immediately broke his embrace and both blushed uncontrollably. Remembering the sense of urgency The Doctor shook of the awkwardness of the situation and when straight to business "why did you call me, is everything all right" trying to ignore the previous situation also Luna's face was the very definition of worry.

"It's Celestia I can't find her anywhere" Twilight was sceptical to say the least about Luna's 'emergency'.

"Princess are you sure she didn't just go out?" Luna nodded but The Doctor noticed something on the floor which made his heart fall.

"I would but I heard my sister scream in the most terrible way possible and when I arrived Celestia and the guards in the throne room where gone" taking the new information into account The Doctor looked around the room and saw ash piles in the guard position and the one in front of the throne.

"This is bad, this is really, really bad" Twilight looked hadn't seen the ash piles but as The Doctor ran up to the first pile exactly where Celestia would be seated Twilight eyes widened in horror.

"Doctor please don't, don't tell me that's…" The Doctor took out his compass and opened it before dropping on his knees.

"Princess Celestia" Luna was completely clueless while Twilight began to tear up and The Doctor's face was too much like it was when Starlight mentioned the Professor.

"Doctor, what's wrong?" but instead of The Doctor answering her question, a figure came from behind the throne and looked towards the three with a blank expression.

"Nothing is wrong dear princess of the night but my rise to power" The Doctor looked up to see this figure whose coat colour was a dull blue and had piercing red eyes.

"Who are you? What have you done with my sister!?" Luna yelled walking closer to the stallion but was held back by The Doctor.

"Luna, there was a similar incident in Ponyville…" Luna looked back at the old stallion, his face was even colder and it was clear he didn't want to say what he had too "I'm sorry Luna, I'm so sorry..." Luan had known The Doctor long enough to know that when he said those words in that way, it was never a good thing. Luna looked on to Twilight who was crying heavily and then towards the ash pile behind her.

"But…But we saw the future, she can't be…" Luna had figured out what The Doctor was getting at and was beginning to break down "Doctor this better be a joke…" The Doctor continued to look at her with a cold look confirming her fears "Celestia…My Sister" Luna collapsed beginning to cry for the loss of her older sister "CELESTIA!" The Doctor didn't show it but deep in his hearts, he mourned the loss of one of his greatest friends and felt anger for the one who caused the pain.

"I hope it helps that the time taken was well spent" The stallion commented who in return earned a glare from the Time Lord.

"You can shove it… cause you just killed one of my best friends and you do not want to know what happens to the people that hurt the ones I care about. So before I kill you, who the Hell are you?" The Doctor demanded with rage in his voice and the stallion took a step back yet showing no emotion on his face.

"I have no title but if I must then you may call me Syphon the time stealer" just as Syphon introduced himself a guard ran in to the room unaware of what was happening yet bearing an important message.

"Your highness! I have an important…" taking a moment he saw both Luna and Twilight crying and a lone stallion staring at him "what the hell…who are you!?" the guard demanded for The Doctor to identify but as the Pegasus turned round back to the assassin syphon, he was gone.

"DAM IT!" The Doctor turned to the guard and pulled out his psychic paper "I am Dr Time Keeper investigating a conspiracy against the crown. Relay your message and I will notify Princess Luna when she calm down" the guard could not stop staring into the age old eyes of the Time Lord and delivered his message.

"Uhh, yes sir…it's Ponyville, the entire population has disappeared" The Doctors eyes widened, there is no way he could move that fast but impossible or not an entire towns worth of ponies have vanished just after Celestia was killed The Doctor would bet his Tardis if this was a coincidence. Trying not to think about those lost The Doctor went to Twilight and tried to snap her out of it.

"Twi look at me…Twilight!" looking up at The Doctor Twilight's eyes were red from the crying.

"Doctor…the princess, I…I can't" The Doctor brought Twilight into a hug and spoke directly in her ear.

"I know but we can't sit here doing nothing. It would be an insult to her memory please Twilight, we need to get to The Tardis" breaking from the hug Twilight wiped her eyes and nodded before The Doctor gave Twilight a key "take this, go to the Tardis and flip the green switches closest to the monitor" The Doctor got up and Twilight grabbed his wing to stop him.

"What about you?" The Doctor like an old man lifted Twilights chin.

"I can't leave Luna here…and she is in no condition to move. I will come back and I will save everyone" feeling hopeful Twilight ran out of the room and back to the Tardis but The Doctor noticed another ash pile were that guard was "So you can manipulate time" he said to himself before kneeling next to Luna.

"Doctor what am I going to do? I can't live without my sister" The Doctor felt her pain and his face showed it

"Yes I know what it's like to lose a sister but we can't stay here, this thing feeds off of time, the more he takes the more he can use. He just wiped out Ponyville and by my guess he is taking a more populated area as we speak. You are in full power, you are too important to lose" Luna looked down in sorrow but stood up proudly.

"You are right, my subjects need me. I must not abandon them" as both left, The Doctor looked on unsure if he could save everyone.

"_I just need to get her to the Tardis, Twilight should be safe. I WILL NOT LOSE ANYONE ELSE"_ he thought to himself but he noticed a glimmer as he past another ash pile, he stopped, in every case everything the victim had turned to ash along with them so what had remained form this one.

"Doctor?" Luna called as she noticed The Doctor looking though an ash pile but his face fell when he picked up a key.

"No…oh Please no!" as Luna looked on she noticed a tear drop into the pile "why me? Twilight I'm so sorry, we never did get that soup" The Doctor replaced the key on the pile and bowed his head in respect then began marching back to the throne room.

"Doctor where are you going!?" The Doctor turned to Luna and she was surprised that he was calm as it was clear he knew the person who was killed.

"Luna, I'm sorry but I have to end this the only way I can" The Doctor then ran back and threw the large doors passing the stained windows and confronting Syphon who was sitting on Celestia's throne.

"I saw you heading here and I assumed you wanted to talk" The Doctor stood across from Syphon with a teared up face.

"Tell me what you want? Please just tell me and it's yours, just please no more deaths" The Doctor had lost control of his emotions and begged the creature to spare the rest of Equestria but Syphon's face was unmoved.

"I want the Timeless one" The Doctor was unsure of who he meant but had a good guess.

"You want me…I'm I time lord, I can potentially live for ever. Then do it take me but leave everyone else alone" Syphon tilted his head and looked over The Doctor.

"You are not him, you have much time to spare but I'm afraid there is no one else, so there is no point in giving me anything" The Doctors Hearts dropped, he had lost another world, he had nothing left. Was this how the story would end "but I will take it" Syphon's mouth hinged and was ready to take his life but a flash of blue moved in front of him and what was left of The Doctors soul shattered.

"No" Luna was standing in front of him and blue energy was slowly flowing from her into Syphon's mouth and every so slowly Luna began to age "Luna please no"

"I heard everything, I have no subjects to protect. So I will protect the one pony I have left…you" The Doctor watched in horror as Luna was turning grey from age and struggling to hold back the pain.

"But I need you, you are the only one I have left" The Doctor placed a hoof on her cheek as she closed her eyes smiling.

"Goodbye Doctor" Luna then began to dissolve into ash but before she could leave the Doctor kissed her softly and broke apart.

"I…I love you too" Luna smiled one last time as she died like the rest of her kingdom.

"She had much time and much to share" Syphon's body began to grow and reform but he failed to notice another figure behind the Doctor.

"You just took the only one I could ever love again away from me…" The Doctor looked up no longer angry but distraught "I can stop you but she will never see me again" but before he could play his final card a much older voice could be heard attracting the attention of both The Doctor and Syphon.

"That's why I'm going to do it" the new arrival was and elder with the same grey coat as The Doctor but with a blue pointy hat and cape with a long white beard "Hello everyone"

"What!?" The Doctors surprise was an understatement as the pony in front of him should have been dead for a millennia.

"Why so surprised, don't you recognise me…actually it should be me that recognises you as you are the younger one, Starswirl the bearded at your service" it was indeed Starswirl the bearded standing in the flesh.

"But your dead" Starswirl raised an eyebrow at The Doctors statement.

"Who told you that!, I just left for a vacation. Seriously you leave for 200 years and suddenly "oh, he must be dead, someone brake out the marble statue" sweet Jesus is that what I look like. Have you heard of a lovely thing I invented, it's called a comb you would love it" after Starswirls rant about The Doctors appearance he turned his attention to Syphon.

"You…you are the timeless one" The Doctor was gob smacked at the sudden revelation but he noticed something odd, he had mentioned Jesus but there was only one that could now that.

"Hello again, it's been a while, how have you been" The Doctor stared at the old stallion in astonishment, he had never visited the wizard and seeing him for real was incredible but The Doctor couldn't shake off the feeling he knew him

"Who are you?" Starswirl turned to the Time Lord with the tell-tale smirk across his face.

"Figuring it out are you, let me save you the head ache. There's a reason I wear a cape" Starswirl then proceeded to remove his blue cape and on his flank was a blue galaxy surrounded by six stars, The Doctors cutie mark.

"But that's…" Starswirl chuckled at The Doctors confusion.

"My cutie mark or yours…why not both. That's right I am a banana!…" Syphon and The Doctor tilted there head at his comment "sorry I meant Doctor…I'm you from your future, I mean com on lad, who has been keeping this place safe before you arrived" Syphon had taken Starswirls distraction to his advantage and snuck up behind him to take his prize but before he could he stopped and time had slowed and eventually stopped with only Starswirl and The Doctor unaffected.

"But this is changing your…our own history" Starswirl shook his head slowly and explained with a smile on his face.

"I'm only here because you saw me here, you will have a future and so will those that have died…that idea, I've spent over three hundred thousand years thinking about it, don't waste your time lad, let an old man who is out of time take the fall" The Doctor didn't understand what was going on, he was Starswirl that as his future. To be what he already was, the old man running towards adventure. He was about to sacrifice himself and he was just not yet.

"Thank you Doctor" He said offering his hoof which the older stallion took in good faith.

"You're welcome Banana" The Doctor again raised his eyebrow in confusion.

"Great I'm going to become a nutter, well three hundred thousand years, you got the excuse" both began to laugh and Starswirl took out a rusty sonic screwdriver and passed it on as gold light began emanating from his body.

"To our last moment, Avanti" he then turned round and allowed Syphon to move once again but instead of running away or using some device to banish him, all he did was hug the creature and the gold regenerative energy was pulled back in feeding Syphon.

"What are you doing, you are giving me exactly what I desire…wait what is this light" it was then that Syphon began cracking and he looked at The Doctor his face still blank as ever "is this death?" in a brilliant flash of light Starswirl regenerated and all of that energy was drawn in by Syphon and lunder the pressure both exploded, the resulting blast destroyed the palace and all of canterlot but The Doctor was still alive surrounded in a force field and the explosion began to slow down.

"How the hell?" The Doctor noticed Starswirls screwdriver had glowing writing on it "a protection spell?" The Doctor then noticed that the explosion began confusing in on itself, time was reversing "as I thought, if he absorbed to much time his abilities would back fire but why did he regenerate?" his question would soon be answered as when everything returned to the night before The Doctor saw a young blue foal with yellow hair lying on the ground asleep "because the energy would have rippled back and regenerate Syphon into a child, therefore wiping his memory" The Doctor walked over to the harmless child, picked him up and took him back to the Tardis.

**Ponyville orphanage 20 years ago**

A young mare unicorn sat at the reception desk not expecting anyone this late in the evening and was about to lock the door but a grey stallion with a messy brown mane walked into the reception hall with a basket in his mouth.

"Hello can I help you" The stallion placed the basket on the desk, he had a pleasant smile with very old eyes for his age.

"Yes I'm here to drop of this child, he needs a home and people to take care of him, tell him when he that his parents loved him very much" the mare was shocked most would leave their children on the door step and leave with nothing but a note.

"May I ask why you rather not take care of him yourself?" the stallion smiled softly as he explained.

"He's not mine and his parents are no longer with us" the mare's heart fell for the poor soul unknowing her death would occur because of the child that slept before her with his destiny about to change, she looked into the basket to see the small child sleeping peacefully but when the mare looked up to speak to the stallion she was surprised when he had left without making a sound. She then lifted the child and inspected him for anything out of the ordinary and placed him in an empty bed with the rest of the children but as she left a bright flash of light lit up the room and on the child's flank appeared an hourglass with Drum and drumsticks together.

**Present day**

Twenty years had passed and the same mare was sitting at her desk glad that the hyperactive children had all gone to school but she looked up as the bell to signal the door opening rang, she was shocked that a grey stallion with the same messy brown mane walked in.

"Hello again" the mare stood up slowly and started at the stallion.

"Hi, can I help you" the stallion had the same soft smile and asked a very odd question that only she could answer.

"I just came to see if he's okay, how did he turn out?" the mare couldn't explain it but this was the same stallion from 20 years ago.

"He grew up well, studying to become a Doctor" this fact made the stallion laugh a bit.

"Wise choice" the stallion looked down like he was remembering.

"Uh was there anything else?" the stallion then looked up taking in a deep breath.

"Yes I would like to make an adoption" the mare smiled and was happy to assist him.

"Well sir, I would be glad to show you the children but they are all at school unless you would like to adopt a foal?" the stallion took out a picture from his bag and handed it to the mare.

"No matter, I already know the child just give her this, on hearts warming day" The mare smiled as she had no objection with his choice, so she grabbed a pen and was about fill out the adoption forms.

"I will need a name sir?"

"Time Keeper, Dr Time Keeper"

**Hearts Warming Day**

On the morning of hearts warming eve, Scootaloo began to stir from the sun shining through the window and onto her face, something she complained about occasionally, as she got up and looked around to see all of the other children still asleep, she noticed a blue letter on her bedside, after opening it she found a note and a brass key. Reading the note she got out of bed and began to pack her things the note had read.

"Scootaloo, if you are reading this it mean I have legally taking you under my care, the orphanage was kind enough to keep you until this day as I thought you'd like I good present.

No one deserves to live without family for you nor for me. I'll be parked outside.

Your new parental unit

The Doctor"

After stuffing all of her stuff into one case, the receptionist and the manager of the home where outside the room watching the filly as she rushed to pack up.

"I feel so happy for her, she always did want her own family" the receptionist said quietly.

"yes and though I disagree with Dr Keepers accommodations, I can't think of anyone better to care for Scootaloo" both mares then left as Scootaloo was about to run out of the door and when she did, standing like it did in the Crystal Empire was the Tardis covered in the snow which bombarded the area the previous night. She then used the key she was given and the wooded door opened with a light click.

**Golden oak library, A Couple Hours Earlier**

Silence lay in the home of Twilight Sparkle as she slept peacefully, dreaming of the exciting things she and her friends would do on one of the most festive times of the year. However her peace would only last so long as the loud groan of an ancient time machine woke Twilight from her slumber.

"Doctor, it's too early, give it three hours" expecting the hyperactive Time Lord to start ranting on. She shot up hearing nothing but the sound of Spike snoring "Doctor?" she looked around unable to see the blue box anywhere, she did see however a small present on her bed side, picking it up she began to remove the wrapper afterwards she was left with a simple brown box with a letter on the top which read.

"_Twilight_

_You have taught and shown me so much about your world, so I thought I'd let you experience a tradition from mine_

_Merry Christmas_

_The Doctor"_

Being the curious thing that she is Twilight lifted the lid of the box and sitting comfortably inside was a photo of her and her friends all huddled together with the Doctor behind them, in the top corner was a written message.

"_A friendship that will last for all Time"_

Receiving a gift like this made Twilight shed a tear in joy "This…This is perfect" she said to herself before getting out of bed and walking down into her living room and using her magic to hang the picture on the wall but she couldn't help noticing the Tardis wasn't in the house "I wonder where he is?"

**Canterlot Palace**

People would assume that winter was Luna's favoured season but since the nights were longer and the temperature below freezing, less ponies would stay out at night and Luna got less sleep but she loved the snow, sadly she usually had no one to play in the snow with her. So as the night went on she sat peacefully under a small tree that was still green even in the harsh cold.

"Beautiful night" Luna turned to see The Doctor land beside her.

"Doctor, this is unexpected more so than your usual antics, what is it this time?" what Luna did not expect more than The Doctors arrival was the fact that he hugged her and for some reason began to cry.

"Doctor? Are you alright?" Luna had been in this situation before with Celestia and the only thing she could do for the silent saviour was comfort him and held him "what's happened?" she had never seen The Doctor like this before and it broke her heart but what the next words The Doctor would say completely shattered it "promise me that you will stay with me and never leave" Luna began to tear up also, he was opening up. What had happened for him to move on from his past failures? Luna and The Doctor both noticed that a plant was growing above them and in a quick look both identified the plant.

"Mistletoe…he he, remind me to give lady luck a call" The Doctor retorted with a chuckle, making Luna giggle.

"Shut up" following the tradition of the infamous plant Luna moved in to kiss The Doctor which he gladly returned, both yet failed to notice a tall slender figure looking at them from afar.

"My little sister has finally grown up" Celestia figured that this moment required something special so using her magic she lowered the moon while raising the sun in parallel creating what Equestria would consider in 1000 years to be the most Beautiful morning in history.

Next Time:

Foreign Similarities 

Courier: that's it people season 1, ending with a major plot twist. Don't worry Starswirl is gone but not for long, he will return more manic than ever

Twitter: /TARDISCourier

Facebook: TheTARDISCourier


End file.
